Definitive restorative management of young permanent molars affected with severe MIH is still elusive with a dearth of conservative restorative options. The present trial compared the 36 months clinical and radiographic performance of minimally invasive cast metal and indirect resin onlays for rehabilitation of permanent first molars affected with severe MIH.In this parallel group open label randomised trial, 42 vital molars affected with severe MIH in 30 children, aged 8-13 years were randomly allocated using stratified permuted block randomization to receive either a cast metal onlay or an indirect composite onlay (n = 21 each). Clinical and radiographic evaluations of these onlays were carried out at 9, 18 and 36 months using the USPHS criteria. Cumulative survival rate as well as the calculated clinical success rates of both types of onlays were also determined. The longevity of onlays was assessed using Kaplan-Meier survival analysis.At 36 months, overall retention rate was found to be 95% with complete elimination of any pre-existing sensitivity. Cumulative survival rates were found to be 95% vs. 100%, p = 0.67, while the calculated clinical success rates were 90% and 85.7% for metal and resin onlays, respectively, with no significant differences (p = 0.76). Mean survival rates based on Kaplan-Meier analysis were determined to be 85% vs. 100% for the metal and composite groups, respectively (p = 0.075).Irrespective of the type of material used, onlays offer a predictable and conservative restorative alternative for molars affected with severe MIH.The trial is registered under Clinical Trial Registry India (CTRI/2016/10/007379).