Background: Many studies have assessed perspectives of medical students toward institutional diversity, but few of them have attempted to map changes in diversity climate over time. Objective: This study aims to investigate changes in diversity climate at a Jesuit medical institution over a 12-year period. Methods: In 1999, 334 medical students completed an anonymous self-administered online survey, and 12 years later, 406 students completed a comparable survey in 2011. Chi-square tests assessed the differences in percent responses to questions of the two surveys, related to three identities: gender, race, and sexual orientation. Results: The 1999 versus 2011 samples were 46% versus 49% female, 61% versus 61% Caucasian, and 41% vs. 39% aged 25 years or older. Findings suggested improvements in medical students’ perceptions surrounding equality ‘in general’ across the three identities (p<0.001); ‘in the practice of medicine’ based on gender (p<0.001), race/ethnicity (p=0.60), and sexual orientation (p=0.43); as well as in the medical school curriculum, including course text content, professor's delivery and student–faculty interaction (p<0.001) across the three identities. There was a statistically significant decrease in experienced or witnessed events related to gender bias (p<0.001) from 1999 to 2011; however, reported events of bias based on race/ethnicity (p=0.69) and sexual orientation (p=0.58) only showed small decreases. Conclusions: It may be postulated that the improvement in students’ self-perceptions of equality and diversity over the past 12 years may have been influenced by a generational acceptance of cultural diversity and, the inclusion of diversity training courses within the medical curriculum. Diversity training related to race and sexual orientation should be expanded, including a follow-up survey to assess the effectiveness of any intervention.