Background: Different in-vitro studies have reported various results regarding shear bond strength (SBS) of orthodontic brackets when SEP technique is compared to conventional system. This in-vivo study was designed to compare the effect of conventional acid-etching and self-etching primer adhesive (SEP) systems on SBS and debonding characteristics of metal and ceramic orthodontic brackets. Material and Methods: 120 intact first maxillary and mandibular premolars of 30 orthodontic patients were selected and bonded with metal and ceramic brackets using conventional acid-etch or self-etch primer system. The bonded brackets were incorporated into the wire during the study period to simulate the real orthodontic treatment condition. The teeth were extracted and debonded after 30 days. The SBS, debonding characteristics and adhesive remnant indices (ARI) were determined in all groups. Results: The mean SBS of metal brackets was 10.63±1.42 MPa in conventional and 9.38±1.53 MPa in SEP system, ( P =0.004). No statistically significant difference was noted between conventional and SEP systems in ceramic brackets. The frequency of 1, 2 and 3 ARI scores and debonding within the adhesive were the most common among all groups. No statistically significant difference was observed regarding ARI or failure mode of debonded speci mens in different brackets or bonding systems. Conclusions: The SBS of metal brackets bonded using conventional system was significantly higher than SEP system, although the SBS of SEP system was clinically acceptable. No significant difference was found between conventional and SEP systems used with ceramic brackets. Total SBS of metal brackets was significantly higher than ceramic brackets. Due to adequate SBS of SEP system in bonding the metal brackets, it can be used as an alternative for conventional system.