A thesis in medicine is a scientific work which allows a medical student to acquire a Doctor of Medicine degree. It is therefore recommended that theses presented by students fulfill essential methodological criteria in order to obtain scientifically credible results and recommendations. The aim of this study was to assess the methodology of thesis presented to the Faculty of Medicine in Fez in 2008. We developed an evaluation table containing questions on the different sections of the IMRAD structure on which these theses were based and we estimated the proportion of theses that conformed to each criterion. There were 160 theses on various specialties presented in 2008. The majority of the theses (79.3%) were case series. Research questions were clearly expressed in 62.0% but the primary objectives were pertinent in only 52.0%. Our study shows that there were important deficiencies in the methodological rigor of the theses and very little representation of the theses in publications.