In medical schools small specialties like clinical pharmacology may be integrated in courses covering larger specialties and examined concomitantly. The results of a pilot study suggested that this approach would have negative consequences on the knowledge gained in clinical pharmacology with integration of this speciality in the course of internal medicine and concomitant examination. The aim of the present study was to assess in more detail whether students' presumed tendency to study selectively influences approval (the pass mark), a surrogate marker of the knowledge gained. A written examination for the integrated course in clinical pharmacology and internal medicine in Gothenburg, Sweden, was specifically designed in 2008 to evaluate the research question. The examination consisted of 50 short answer questions, of which five focused on clinical pharmacology (maximum score 10) and 45 were on internal medicine (maximum score 90). The cut-off level for approval (pass mark) was 60 %. Of the 81 students who wrote the examination, 73 (90.1 %) passed the examination as a whole. When the questions in clinical pharmacology were assessed separately, 62 (76.5 %) students passed the cut-off level of 60 %; the corresponding proportion of students achieving the cut-off level for questions on internal medicine was 90.1 %. There was a significant correlation between the results of the two specialties (p < 0.001), but the questions on clinical pharmacology generated lower scores (p < 0.001). The correlation coefficient between the results of two randomly chosen questions for clinical pharmacology was greater than that of two randomly chosen questions in internal medicine (p < 0.001). Our results confirm that a small specialty like clinical pharmacology may need to be examined separately in order to guarantee a sufficient level of knowledge among students.