Background: Medical training focuses heavily on clinical skills but lacks in training for navigating challenging clinical scenarios especially with regard to diversity issues. Our objective was to assess third-year medical students' preparedness to navigate such scenarios. Methods: A 24-item survey was administered electronically to third-year medical students describing a range of specific interactions with patients, peers, and "upper-levels" or superiors including residents and attendings, spanning subjects including gender, race/ethnicity, politics, age, sexual orientation/identity, disability, and religion. Students rated their level of comfort via a 5-point Likert scale ranging from 1 ("Very Uncomfortable") to 5 ("Very Comfortable"). Basic demographics were collected and data were summarized for trends. Results: Data were analyzed from 120 students (67% response rate, 54.2% female, 60.8% non-Hispanic white). Students reported lower comfort with peer and superiors compared to patient interactions (p < 0.0001). Students reported the highest comfort with sexual orientation/identity-and religion-related interactions (median (IQR): 3.3 (1.3) and 3.4 (10.0), respectively) and the lowest comfort with gender-, race/ethnicity-, and disability-related interactions (median (IQR): 2.3 (1.3), 2.0 (1.0), 2.5 (1.5), respectively). Males reported significantly higher median comfort levels for scenarios with upper-level, gender, and religion related interactions. Males were more likely to be completely comfortable versus females across the 24 scenarios, although multiple male response patterns showed evidence of a bimodal distribution. Conclusions: Third-year medical students report generally inadequate comfort with navigating complex clinical scenarios, particularly with peers and supervisors and relating to gender-, race/ethnicity-, and disability-specific conflicts. There are differences across gender with regards to median comfort and distribution of scores suggesting that there is a subgroup of males report high/very high comfort with challenging clinical scenarios. Students may benefit from enhanced training modules and personalized toolkits for navigating these scenarios.