Purpose: To investigate the association between poor performance on National Board of Medical Examiners clinical subject examinations across six core clerkships and performance on the United States Medical Licensing Examination Step 3 examination. Method: In 2012, the authors studied matriculants from the Uniformed Services University of the Health Sciences with available Step 3 scores and subject exam scores on all six clerkships (Classes of 2007-2011, N = 654). Poor performance on subject exams was defined as scoring one standard deviation (SD) or more below the mean using the national norms of the corresponding test year. The association between poor performance on the subject exams and the probability of passing or failing Step 3 was tested using contingency table analyses and logistic regression modeling. Results Students performing poorly on one subject exam were significantly more likely to fail Step 3 (OR 14.23 [95% CI 1.7-119.3]) compared with students with no subject exam scores that were 1 SD below the mean. Poor performance on more than one subject exam further increased the chances of failing (OR 33.41 [95% CI 4.4-254.2]). This latter group represented 27% of the entire cohort, yet contained 70% of the students who failed Step 3. Conclusions: These findings suggest that individual schools could benefit from a review of subject exam performance to develop and validate their own criteria for identifying students at risk for failing Step 3.