There has been no literature on analysing short answer questions (SAQs) to assess how well the students captured the essence of core concepts in basic sciences disciplines. The objective of this study was to assess the performance of students and marking process in core concept-intensive SAQs on physiology and pathology in a professional examination of the undergraduate medical curriculum. Two faculties, each from physiology and pathology disciplines identified the core concept-intensive SAQs. Consensus was taken on how core are the concepts and a marking scheme was developed by ranking of the elements of the concept. Based on their overall performance, top 20 students, middle 20 students and bottom 20 were identified, and their answers were graded (parameters: not attempted, wrong concept, incomplete or irrelevant, and how well the essence of critical key concepts was captured). This communication focused on the discrepancies in the marks awarded by the marker (examiner) and by the investigators. The discrepancy was higher in the middle 20 group while most of the bottom 20 had no marks awarded as they had not attempted or had a wrong or irrelevant concept. The construction of model answers in the examinations should be improved to unlock how much students could capture the underlying key critical concepts. Alternatively, the marker should be a content expert capable of going beyond the given model answer.