Background: The principle of pulp treatment in primary dentition is that tooth should remain in mouth in a non-pathological healthy condition to fulfill its role in primary dentition. The present study was conducted to compare formocresol and mineral trioxide aggregate in deciduous teeth. Materials & Methods: It comprised of 40 deciduous molar of children aged 4- 8 years of age. The study protocol was approved from institutional ethical committee. A written consent was obtained from parents of children. General information such as name, age, gender etc. was recorded. Patients were divided into 2 groups of 20 each. In group I, pulpotomy was done with formocresol and in group II, pulpotomy was done with MTA. Teeth were compared clinically at 3 months and 6 months intervals. Results: Patients were divided into 2 groups of 20 each. In group I, pulpotomy was done with formocresol and in group II, pulpotomy was done with MTA. Results showed that there was comparatively less pain, fistula formation, abscess and mobility in group II as compared to group I recorded at 3 months and 6 months (P< 0.05).Conclusion: Mineral Trioxide Aggregate (MTA) found to be better as compared to formocresol. There was less pain, fistula formation, abscess and mobility. Key words: Formocresol, mineral trioxide aggregate