Abstract Background The mini clinical evaluation exercise (mini-CEX)—a tool used to assess student-patient encounters—is increasingly being applied as a learning device to foster clinical competencies. Although the importance of eliciting self-assessment for learning is widely acknowledged, little is known about the validity of self-assessed mini-CEX scores. The aims of this study were (1) to explore the variability of medical students’ self-assessed mini-CEX scores, and to compare them with the scores obtained from their clinical supervisors, and (2) to ascertain whether learners’ self-assessed mini-CEX scores represent a global dimension of clinical competence or discrete clinical skills. Methods In year 4, medical students conducted one to three mini-CEX per clerkship in gynaecology, internal medicine, paediatrics, psychiatry and surgery. Students and clinical supervisors rated the students’ performance on a 10-point scale (1 = great need for improvement; 10 = little need for improvement) in the six domains history taking, physical examination, counselling, clinical judgement, organisation/efficiency and professionalism as well as in overall performance. Correlations between students’ self-ratings and ratings from clinical supervisors were calculated (Pearson’s correlation coefficient) based on averaged scores per domain and overall. To investigate the dimensionality of the mini-CEX domain scores, we performed factor analyses using linear mixed models that accounted for the multilevel structure of the data. Results A total of 1773 mini-CEX from 164 students were analysed. Mean scores for the six domains ranged from 7.5 to 8.3 (student ratings) and from 8.8 to 9.3 (supervisor ratings). Correlations between the ratings of students and supervisors for the different domains varied between r = 0.29 and 0.51 (all p < 0.0001). Mini-CEX domain scores revealed a single-factor solution for both students’ and supervisors’ ratings, with high loadings of all six domains between 0.58 and 0.83 (students) and 0.58 and 0.84 (supervisors). Conclusions These findings put a question mark on the validity of mini-CEX domain scores for formative purposes, as neither the scores obtained from students nor those obtained from clinical supervisors unravelled specific strengths and weaknesses of individual students’ clinical competence.