Purpose: The purpose of this study was to identify students’ perceptions of the curriculum in two different cohorts who received two different delivery styles (system-based or problem-based) of physical diagnosis curriculum to determine if significant differences were present, and to identify how each cohort performed on their clinical experiences (CEs). Methods: One-hundred and sixteen students at one physician assistant (PA) program from two cohorts of students were surveyed using a true/false survey (analyzed by chi-square) regarding their perceptions of their preparedness for clinical rotations with regard to the ability to perform physical examinations. Clinical preceptor evaluations were also analyzed for both cohorts with respect to competence in physical examination skills as rated by preceptors on a scale of 1 to 3. Results: Each cohort related that they were satisfied with their preparation regardless of delivery format, with no tendencies toward respective cohorts indicating they should have received the alternate delivery format. No significant differences were found in the students’ perceptions of their ability to perform a physical examination on CEs between the cohorts or between the groups’ performances on their CEs. Conclusions: System-based and problem-based formats were found to have merit and similar outcomes and thus can both be deemed effective teaching methods for teaching physical diagnosis curriculum.