Medical education research in general is a young scientific discipline which is still finding its own position in the scientific range. It is rooted in both the biomedical sciences and the social sciences, each with their own scientific language. A more unique feature of medical education (and assessment) research is that it has to be both locally and internationally relevant. This is not always easy and sometimes leads to purely ideographic descriptions of an assessment procedure with insufficient general lessons or generalised scientific knowledge being generated or vice versa. For medical educational research, a plethora of methodologies is available to cater to many different research questions. This article contains consensus positions and suggestions on various elements of medical education (assessment) research. Overarching is the position that without a good theoretical underpinning and good knowledge of the existing literature, good research and sound conclusions are impossible to produce, and that there is no inherently superior methodology, but that the best methodology is the one most suited to answer the research question unambiguously. Although the positions should not be perceived as dogmas, they should be taken as very serious recommendations. Topics covered are: types of research, theoretical frameworks, designs and methodologies, instrument properties or psychometrics, costs/acceptability, ethics, infrastructure and support.