Introduction: Evidence suggests that pre-clerkship courses in clinical skills and clinical reasoning positively impact student performance on the clerkship. Given the increasing emphasis on reducing diagnostic reasoning errors, it is very important to develop this critical area of medical education. An integrated approach between clinical skills and clinical reasoning courses may better predict struggling learners, and better allocate scarce resources to remediate these learners before the clerkship. Methods: Pre-clerkship and clerkship outcome measures from 514 medical students graduating between 2009 and 2011were analyzed in a multiple linear regression model. Results: Learners with poor performances on integrated pre-clerkship outcome measures had a relative risk of 6.96 and 5.85 for poor performance on National Board of Medical Examiners (NBME) subject exams and clerkship performance, respectively, and explained 22 % of the variance in clerkship NBME subject exam scores and 20.2 % of the variance in clerkship grades. Discussion: Pre-clerkship outcome measures from clinical skills and clinical reasoning courses explained a significant amount of clerkship performance beyond baseline academic ability. These courses provide valuable information regarding student abilities, and may serve as an early indicator for students requiring remediation. Conclusions: Integrating pre-clerkship outcome measures may be an important aspect of ensuring the validity of this information as the pre-clerkship curriculum becomes compressed, and may serve as the basis for identifying students in need of clinical skills remediation.