Assessment is fundamental to the educational process. Multiple choice questions (MCQs) and short essay questions (SEQs) are the most widely used assessment method in medical school. The current study evaluated the discriminating value of SEQs compared to MCQs as assessment tools in clinical biochemistry and correlated undergraduate students' SEQ scores with their overall scores during the academic years 2021-2022 and 2022-2023. This is a descriptive-analytical study in which MCQ and SEQ papers of clinical biochemistry were analyzed. The mean score for SEQs in males was 66.7 ± 1.2 and for females it was 64.0 ± 1.1 SEM, with a p-value of 0.09; for MCQs, the mean score for males was 68.5 ± 0.9 SEM and for females it was 72.6 ± 0.8. When analyzing the difficulty index (DI) and discrimination factor (DF) of the questions, MCQs have a mean DI of 0.70 ± 0.01,and DF of 0.05 to 0.6. SEQs have a mean DI of 0.73 ± 0.03 and DF of 0.68 ± 0.01; there was a significant difference between the DF of MCQs and SEQs (p < 0.0001). Furthermore, there was a significant difference between SEQs and MCQs when categorizing students based on their scores, except for A-scored students. According to the current study, SEQs have a higher discriminating ability than MCQs and help differentiate high-achieving students from low-achieving students.