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The Methodology section of a thesis or dissertation (also sometimes called the Methods or Materials and Methods section) is where you explain the exact procedures you used to conduct your research. It should be very detailed - after completing this section the reader should be able to recreate the work that you did. The people reading and evaluation
your dissertation will be looking closely at your methods to make sure your work is sound, so you want to make sure this section is clear and complete.
The Sciences and Engineering
The Methodology section in papers that cover investigative work in the sciences and engineering is a thorough explanation of the experimental design. You want to provide a detailed description not just of how your study was done, but also why that particular experimental design was chosen. The writing should be detailed but concise. Don't include information that isn't required to repeat the experiment, and don't over-explain concepts or techniques that will already be familiar to those in your field. As with the rest of the paper, the methodology should be in the third person and in past tense.
When describing your study, make sure it includes the following elements:
Research design.
Start by outlining the basic style of your research. Is the research experimental? Is it correlational, causal comparative, or a mixed design? What variables will you be looking at? How have you accounted for bias or uncontrollable variables? Did you use any randomization techniques? Also address how the research design you chose is appropriate for the question you're trying to answer. No matter what field you're in, there are likely many study techniques for you to choose from, so make sure the reader understands why you picked the methods you did. Setting and Materials.
Describe the materials used in your study and the setting where it took place. For an experimental study in a field such as biology, this section would include things like the lineage of plants, animals, or cells involved in the experiment, a description of laboratory or field conditions, and details of the equipment used. In the social sciences, this might mean a description of the population being studied as well as details on sample size - basically, anything the reader would need to know to accurately recreate your work.
Remember that you need to very specific about your materials. If you used animals in your study, you can't just say "mice." You need to include details like age, gender, and familiar relationship. If you conducted a survey, you need to specific about the exact age, gender, and number of subjects. Also make sure to be specific about your equipment. If you used a particular software package or a lab aparatus, you need to tell the reader it's exact name. However, you won't usually need to include brand names unless that particular item varies significantly by manufacturer.
Ethical considerations.
If you're doing work with animals or human subjects, you'll need to include in your methods a section discussing how you addressed ethical consideration. This will likely need to contain a statement that your institution's review board has approved your research protocols. Pilot study.
Often in the social sciences, instruments like surveys have to be tested for accuracy and usefulness before they can be used to address the main research question. If your work includes this type of pilot study, you need to include that information in the Methodology. For example, if a pilot study was used to develop a questionnaire, you would need to detail how the questionnaire was developed, how it was tested and evaluated, and how that evaluation effected your use of the questionnaire later in your work. Procedure.
Once you're described the materials used you'll need to detail how the experiment was carried out and how data was collected. The method of data collection is a key part of being able to recreate a study, so it's important you specify the how, where, when, and why of your methods for collecting and recording data. Much like in the materials section, you'll need to be very specific so the experiment could be recreated if necessary.Analysis.
After the data was collected how was it analyzed? Include details of any statistical techniques used as well as your rationale for choosing particular methods of analysis. Everything that follows in your discussion will stem from the analysis of your results, so make sure the reader knows that the analysis is accurate. If you transformed data, you need to explain why and how. If you calculated correlation or used other statistical tests, explain your threshold for significance. Summary.
Finish the Methodology section with a brief conclusion that reminds the reader of your general research design and that leads into the Results section.
To make sure your methodology is complete ask yourself whether it answers these basic question:
- What was done to answer the research question?
- How was the work done?
- Is your experimental design justified?
- How were the results analyzed?
The Humanities
The Methodology section in papers for the humanities is usually significantly shortened or left out altogether. When a methods section is included, it should be used to describe your research techniques and/or the theoretical approach you've taken in addressing your research question.
Research methods.
Outline how you performed any research included in your dissertation. For example, how did you locate and authenticate sources? How did you decide which works to include or leave out of your research? This section can be necessary if you're doing original research, but don't confuse this with the
literature review - you want to discuss how the research was done, not what you uncovered.
Theoretical approach.
Describe the theoretical approach you've taken to address your research question. If you're writing a dissertation in literature, for example, you might be discussing texts in terms of a particular ideology such as Marxism or post-structuralism. Similarly, a dissertation in history might use the methodology section to highlight opposing interpretations of a primary source and to show the reader why you've chosen one approach over the other. 
