Conservative procedures using dentin bonding agents are one of the important aspects of paediatric dental practice. The objective of this in vitro study was to comparatively evaluate the microleakage of two self etching adhesives in primary and permanent teeth. Materials and methods Sixty-four human anterior teeth (thirty-two primary and thirty-two permanent) were divided into four groups: primary teeth bonded using a 6th generation (Contax) bonding agent; permanent teeth bonded using a 6th generation (Contax) bonding agent; primary teeth bonded using a 7th generation (Clearfil S3) bonding agent; permanent teeth bonded using a 7th generation (Clearfil S3) bonding agent. A Class V cavity was prepared on all samples and were restored with composite resin as per manufacturers’ instruction. After thermocycling, the teeth were stained with methylene blue, sectioned, and measured for microleakage. Results It was found a statistically significant difference in microleakage between incisal and gingival margins in each of the study group. Conclusion Clearfil S3 (7th generation) bonding agent could be of greater advantage in paediatric dentistry than Contax (6th generation) because of its fewer steps and lesser microleakage in both primary and permanent teeth.