In postgraduate study, students including L2 students are often required to write a thesis and, as a growing literature reveals, L2 students often experience difficulties in the writing of this genre. While most of this research has involved surveys (questionnaires and interviews) and case studies of supervisor perceptions, only a few studies have also considered student perceptions. Most of the perceptions have considered student difficulties when writing the thesis as a whole, rather than particular section. The present study, based on the use of in-depth interviews with four supervisor-student pairs, focused on student difficulties in writing the discussion of results section (DRS) of the thesis and investigated the extent to which the perceptions of the students matched those of their supervisors. The study found that: (1) students had a more limited understanding of the function of the DRS compared to that of their supervisors; (2) common understanding between the supervisors and the students about the nature and cause of the students' difficulties was limited; and (3) students tended to use limited proficiency as a default mode of explanation of their difficulties whereas three out of the four supervisors offered explanations not related to second language proficiency. (Contains 4 tables.)