Since a very long time, a significant number of patients have been seeking treatment at Complementary and Alternative Medicine health facilities, but the disease burden at these facilities has never been assessed and documented. Present cross-sectional study was carried out at Ayurvedic tertiary care hospital to document and to assess the rationale of disease reporting at Ayurvedic institutions of the northern state of India from January 2011 to October 2011. Almost half of the patients′ morbidities were not classified at all into any of the disease categories. The common reported morbidities at study hospital were: Respiratory (10.5%), neuromuscular (9.5%), digestive (9.2%) and circulatory (9.1%) disorders. As the majority of diseases were unclassified, so mainstreaming of the effective disease surveillance would be required to understand the morbidity pattern and successful treatment practices at health facilities.