The purpose of the present pilot study was to evaluate the benefits of innovative teaching methodologies introduced to final year occupational and physical therapy students in Christian Medical College in India. Students' satisfactions along the long-term retention of knowledge and clinical application of the respiratory anatomy have been assessed. The final year undergraduate physical therapy and occupational therapy students had respiratory anatomy teaching over two sessions. The teaching involved case-based learning and integrated anatomy lectures (vertical integration) with the Anatomy department. Pretest and immediate and follow-up post-tests were conducted to assess the effectiveness of the innovative methods. A feedback questionnaire was marked to grade case-based learning. The method of integrated and case-based teaching was appreciated and found to be useful in imparting knowledge to the students. Students retained the gained knowledge adequately and the same was inferred by statistically significant improvement in both post-test scores. Vertical integration of anatomy in the final year reinforces their existing knowledge of anatomy. Case-based learning may facilitate the development of effective and clinically sound therapists.