Writing a research paper is both a skill and an art. Among its key components, the methods section plays a vital role, making it the foundation of effective scientific writing. If you're like many early-career researchers who think the methods section is the easiest part to write and doesn’t need much thought, this article will show why that assumption is incorrect.

At some point in your academic journey, you’ve probably asked your mentor, colleagues, or even a search engine, “How do I write the methods section of a research paper?”

Don’t worry, you’re not alone. Even experienced researchers often struggle to decide what experimental details to include, which can lead to confusion and frustration.

Furthermore, many academic journals require a methods section that is selective yet descriptive enough to meet their specific guidelines. This makes understanding how to write this section not just important but essential for the success of your paper. Contrary to the misconception that the methods section is just a dull, heavily detailed part of the paper, it should instead highlight the reliability and validity of your research.

Still wondering why the methods section is so crucial to any scientific investigation? Imagine reading a research paper without its methods section.

Even with the data and literature review at your disposal, could you replicate the study or trust its findings?

Likely not. And that’s exactly why this section is indispensable.

Once the importance of the methods section is clear, the next step is understanding how to write one that ties the entire study together. The methods section, previously referred to as Materials and Methods, serves to explain how the researchers addressed the main “research question.” The goal is to provide a clear and detailed account of the study’s design, including the reasoning behind chosen procedures, the experimental setup, the variables involved, the research protocol followed, tools and equipment used, methods of measurement, and the process of analyzing the data collected.

This article explores this topic in depth and offers a comprehensive guide on crafting the methods section of a research paper. To ensure clarity and ease of understanding, the subject has been divided into sections with relevant subheadings.

What is the methods section of a research paper? 

The methods section is a critical part of any research paper because it explains the ‘what,’ ‘how,’ ‘which,’ and ‘why’ behind the study’s approach. This section is essential for understanding how the research led to its conclusions. In a typical research paper, the methods section comes right after the introduction, which provides context for the study, and before the results and discussion sections.

In the methods section, researchers clearly describe what steps were taken, how those steps were executed, what equipment, tools, or techniques were used, how measurements or calculations were performed, and why specific protocols, software, or analytical methods were chosen.

Why is the methods section important?

The methods section serves a key purpose in any research paper: it provides the necessary details about the experimental process, allowing readers to understand the results in context and replicate the study if needed. This section enables readers to assess the reliability and validity of the research. Essentially, it acts as the blueprint of the study, offering clarity to researchers who may need to revisit any part of the research to establish its context or confirm its credibility.

A well-constructed methods section is critical to the success of a research article. An incomplete or unclear description of methods can lead to early rejection or require significant revisions during the publication process. Reviewers often focus on the methods section to evaluate the soundness of the research design and the techniques used for data collection and analysis. In essence, this section showcases the author’s research skills and expertise in their field, making it a crucial component of the paper.

Structure of methods section of a research paper

Like the rest of the research paper, the methods section follows a set structure. This may be influenced by the specific journal guidelines or organized chronologically or thematically, depending on the type of study. When writing the methods section, authors should keep in mind that they are telling the story of how the research was conducted. It’s important to include only the relevant details to prevent confusion and focus on information that helps link different parts of the research together. It’s usually best to present experiments in the order they were done, as this creates a clear, logical flow and makes it easier for readers to follow the study’s progression.

It’s also crucial to explain the reasoning behind each experiment and how the results of earlier experiments influenced the design or interpretation of later ones. This helps readers understand the overall purpose of the research design and the role of each experiment within it. However, depending on the research question and methods, it may be more logical to present the information in a different order. Authors should choose the structure and approach that best fits their study.

If there’s a lot of information to cover, break it into smaller sections with subheadings for better organization. If journal guidelines impose a word limit, extra important details can be included in supplementary files. A good way to structure the methods section is to start with the general approach (what was done), then describe the data collection methods (how it was done), explain the data analysis (how the data was analyzed), and finally, discuss the reasoning behind the chosen methods. These steps will be explained in more detail in the following sections.

How to write the methods section of a research paper

Contrary to common belief, the methods section of a research paper should be written after the study is finished to ensure that no important details are overlooked. It’s essential to complete all relevant experiments before starting to write this section. The next step is to refer to any relevant academic style guides or journal-specific instructions to ensure the methods section is formatted correctly. Typically, this section is divided into materials and methods, with the information organized under each category.

The materials section covers the samples, materials, treatments, and equipment used, while the methods section includes details about the experimental design, sample preparation, data collection, and analysis. Depending on the study’s nature, additional subsections may be needed, such as ethical considerations (like the Declaration of Helsinki for studies involving human subjects), participant demographics, and any other information that could influence the study’s results. Simply put, the methods section has two main components: content and format. Here's an easy checklist to help you if you're unsure how to write this section:

Content:

• Describe the research design, subjects, and sample details

• Include inclusion and exclusion criteria

• Mention any ethical approval or permissions needed for the study

• Provide details about materials, experimental setup, tools, and software used

• Explain data collection and analysis methods

• Address how biases were minimized or confounding variables were controlled

• Justify the experimental procedures used to answer the research question

Format:

• Provide clear and detailed descriptions of each experiment

• Use flowcharts, tables, or infographics to present complex information

• Write in the past tense to indicate completed experiments

• Follow academic style guides (such as APA or MLA) to structure the section

• Include citations according to standard practices in the field

Now that you understand how to write the methods section, let’s look at another common challenge, what exactly to include. Deciding how much detail is too much when writing the methods section can be tricky. In the next section, we’ll explore this issue and discuss possible solutions.

What to include in the methods section of a research paper

The methods section can be challenging to write clearly and concisely due to its technical nature. Many new researchers struggle with staying on topic, often getting caught up in small, unnecessary details that make the text harder to follow and disrupt the flow. The best way to write the methods section is to begin with the most important parts of the experiments. If you're unsure what to include, focus on the details that are essential for understanding the context and for replicating the results. Taking a top-down approach helps ensure that key information is included, without getting lost in the technicalities. Additionally, include details that are necessary for assessing the study’s validity and reliability. Here’s a simple checklist to guide you, and you can also create your own checklist to make sure you don’t miss any important information.

• Structuring the methods section: It’s important to follow the guidelines provided by the journal and any specific instructions for authors. Journals often have specific rules for formatting the methods section. For instance, Frontiers in Plant Sciences suggests organizing the materials and methods section using subheadings and citing relevant literature. In the biomedical field, several standardized checklists are available depending on the type of study. These include CONSORT for randomized clinical trials, PRISMA for systematic reviews and meta-analyses, and STROBE for observational studies. Before writing the methods section, check if there’s a checklist specific to your field to guide you.

• Organizing sections to tell a story: Once you understand the required format for your methods section, you can begin organizing the content logically. As mentioned earlier, you can choose to arrange the sections chronologically or thematically. If you opt for a chronological order, describe the methods in the sequence the experiments were conducted. For example, in an animal study, the methods section should first include details about the species, weight, sex, strain, and age. Then, mention the number of animals, their initial conditions, and housing conditions. Next, explain how the groups were assigned and describe any interventions (such as drug treatments or stressors). Finally, include the tools and techniques used to measure, collect, and analyze the data. If your study involves animals or humans, an ethics approval statement should also be included. When experiments don’t follow a clear order, it’s best to organize them thematically.

• Define and Explain the Objects and Procedure: The experimental procedure should be explained clearly in the methods section. This includes detailing the samples, necessary preparations (such as treatments or drugs), and the methods used to manipulate them. It’s also important to define all variables—control, dependent, independent, and confounding. Confounding variables, in particular, should be explained if they might impact the study’s outcome.

• Match the Order of the Methods Section with the Results: While not required, organizing your paper in a clear and logical way can make it easier to read and understand. Keeping a consistent structure throughout the manuscript helps readers follow along and see how the methods and results connect. One way to do this is by using experiment names as headings in both the methods and results sections. This makes it easier for readers to find and compare specific details across sections.

• Always Include Relevant Information: The methods section should cover all the experiments done, with clear details provided. If the journal has strict word limits, ask if you can include additional information in supplemental files or external repositories. For example, Nature Communications encourages authors to upload detailed protocols to Protocol Exchange, an open-resource depository. This helps make the research more transparent and reproducible by linking the step-by-step protocols to the manuscript when it’s published.

• Pay Attention to the Details: The methods section should provide a clear and detailed list of all materials, tools, instruments, and software used in the experiments. Be sure to mention the equipment used to collect data, including its manufacturer and location (city and state). If any stimuli were used to alter the variables, include those as well. Describe the research process you followed, and if you used a standard protocol, reference earlier studies that used the same protocol. If any modifications were made to the protocol, explain those changes and include any factors considered when planning the study or gathering the data. If new or adjusted methods were used, authors should explain them thoroughly. Readers often rely on the cited literature to assess the reliability and accuracy of the methods, so providing a recognized checklist can help support the credibility of your approach. Don’t forget to include a sample size estimation if necessary. This helps the reader understand how many subjects are needed to detect the expected outcome within a certain level of confidence.

• Consider the Audience: When writing the methods section, it’s important to keep the target audience in mind. Some readers may not understand the reasoning behind certain procedures, especially if the audience is more general. Therefore, it’s a good idea to explain the objective of each procedure in relation to the research question or the overall protocol, especially when there might be uncertainty about the reasoning.

• Data Analysis and Interpretation: Include detailed information about how the data was processed and analyzed, along with the statistical tests used, their significance levels, and the software or tools employed. It’s also helpful to mention whether an experienced statistician’s advice was considered. Be sure to justify the statistical method chosen for the study, explaining why it was the best option and what significance it holds in your research.

What NOT to include in the methods section of a research paper

When writing the methods section of a research paper, it's important to focus on what should be included and what should be left out. Below are key things you should avoid when drafting this section:

• Don’t Over-explain Standard Procedures: Avoid going into too much detail about commonly used methods or techniques that are already well-known and documented in previous studies. Instead of describing these methods in full, simply reference the relevant literature or mention that the manufacturer's instructions were followed.

• Don’t Include Unnecessary Details: Don’t waste space by including irrelevant specifics about the materials or procedures that don’t impact the results. For instance, you don’t need to mention the brand of the water bath used for incubation if it does not affect the outcome of the experiment.

• Don’t Discuss the Results: The methods section is not the place for discussing your findings or referring to tables and figures. Keep this section focused on describing the methods used for the study. Save any analysis or interpretation of results for the results and discussion sections.

• Don’t Make the Section Too Long: For complex methods and procedures, provide the key details in the main text and include any additional information in the supplemental files. Your writing should be clear and concise, maintaining the flow of the methods section without unnecessary information.

Writing a clear and precise methods section is crucial for allowing others to replicate your research or verify your findings. We hope this guide has helped clarify how to structure and write this section effectively, providing you with a better understanding of its purpose.