Vertical integration is believed to increase motivation by providing context for the learning. In this quasi-experimental study, cohort I took two horizontally integrated modules: structure and function of head, neck, and special senses in the second year, and pathophysiology and clinical sciences in the third year. Cohort II took a combined, vertically integrated module in the second year. Data from the questionnaire and examination scores were compared. Response rate was 80.1% (125/156) for cohort I and 57.6% (98/170) for cohort II. Response to the statement that vertical integration provides context to basic sciences was mixed with a higher agreement in cohort II (51.5 vs. 37.2%; P 0.04). Cohort II was least satisfied with the appropriateness of self-study time (52.0 vs. 34.7%; P 0.01). However, cohort II felt that the basic sciences lectures (90.8 vs. 69.4%; P 0.01) and the clinical skills sessions (85.7 vs. 62.1%; P 0.01) were more effective. Cohort II was less satisfied with clinical lectures (80.6 vs. 56.1%; P 0.01) and was less confident in achieving clinical learning objectives (72.8 vs. 40.8%; P 0.01). Mean multiple-choice questions and problem-based learning scores were similar. However, the short-answer question score was higher for cohort I [82.48 (SD 14.9) vs. 70.74 (SD 17.9); P 0.01]. Overall, the idea of early vertical integration had a mixed response. It improved the effectiveness of basic sciences lectures and clinical skills sessions. Achievement of clinical learning outcomes was compromised. A disparity in the module's duration and curricular content, and students' ability to grasp clinical concepts and faculty's expectations are the possible reasons. Increased duration and better communication with clinical faculty may improve early introduction of vertical integration.