Writing in a second (L2)/foreign language is generally a challenging activity, and writing an MA thesis, as an example of academic enterprise, can be daunting when done in a language in which the writer is not fully competent. The challenge such a genre of writing poses for L2 writers has not been properly addressed. To fill in the gap in this area, the present study aimed at comparing Master's theses written by Teaching English as a Foreign Language (TEFL) students in three Iranian universities in terms of the challenges such academic writing poses for student-writers. The corpus comprised 60 randomly selected theses from those universities submitted to English as a Foreign Language departments between the years 2010 and 2012. A series of one-way ANOVAs were employed to compare the means of obtained frequencies across the theses. Results revealed that, except for organisational problems, theses varied in terms of language, style, content and methodological problems. It was also found that theses mainly suffer from style and language problems. The study sheds light on the extent to which L2 writers are aware of the structure of MA theses, reveals the challenges common to most students in this particular type of academic writing and offers advice on improving the quality of thesis-writing.