Many studies indicate that increases in cognitive ability, maturity and educational experience lead to a general increase in moral reasoning skills. However, research has shown that moral development does not occur during medical school and that it may, in fact, plateau or even regress. There is no empirical evidence as to what might be the cause of such a result. The present study aimed to assess moral judgement competence in medical students and to investigate trends in moral judgement competence in relation to age, gender, culture, religion, year of medical course and different programmes within the medical curriculum. We employed a cross-sectional and descriptive design over two consecutive years (2011 and 2012). Students completed Lind's Moral Judgement Test (MJT), which is based on Kohlberg's stages of moral development and is used to measure moral judgement competence (C-INDEX). C-INDEX results were analysed in relation to age, gender, cultural background, religion, cohort and specific programmes within the medical curriculum. The numbers of students who completed the MJT in 2011 and 2012 were 394 and 486, respectively. The two studies showed a significant difference and negative correlations between the moral judgement competence of medical students and both age and year of medical course (p<0.001). The findings suggested the existence of a phenomenon known as 'moral segmentation', which increased significantly as students progressed through medical education, and were significantly linear between cohorts. Students show a decline in moral judgement competence during medical education. This probably reflects an increase in moral segmentation rather than an inhibition in moral development. The challenge is to develop a curriculum that will enable medical students to maintain, or better, increase their moral judgement competence.