The aim of this in vitro study was to compare microleakage of orthodontic brackets between enamel-composite and composite-bracket interfaces at the occlusal and gingival margins, bonded using indirect bonding systems with that of a conventional direct bonding method. Forty freshly extracted human maxillary premolar teeth were randomly divided into two groups. In group 1, the brackets were bonded to teeth directly according to the manufacturer's recommendations. Group 2 consisted of 20 teeth bonded indirectly with Transbond XT (3M-Unitek), as the adhesive, and Sondhi Rapid Set A/B Primer (3M-Unitek), a filled resin primer. After bonding, the specimens were further sealed with nail varnish, stained with 0.5 per cent basic fuchsine for 24 hours, sectioned and examined under a stereomicroscope, and scored for microleakage at the enamel-composite and composite-bracket interfaces from both the occlusal and gingival margins. Statistical analyses were performed using Kruskal-Wallis and Mann-Whitney U-tests with Bonferroni correction. The gingival sides of group 1 displayed a higher median microleakage score than the occlusal side at the enamel-composite interface but this was not statistically significant (P > 0.05). All occlusal margins in both groups showed no microleakage under orthodontic brackets at the enamel-composite or composite-bracket interfaces. Comparisons of the microleakage scores between the direct and the indirect bonding groups at the enamel-composite and composite-bracket interfaces indicated no statistically significant microleakage differences at the gingival and occlusal margins (P > 0.05). The type of bonding method (direct versus indirect) did not significantly affect the amount of microleakage at the enamel-composite-bracket complex.