The purpose of this study was to evaluate the effects of an antimicrobial varnish on the shear bond strength (SBS) of metallic orthodontic brackets bonded with an indirect bonding resin. For this purpose, 60 noncarious human premolars were divided into three equal groups. Group 1 was an indirect bonding control group and, after acid etching of the enamel, the brackets were indirectly bonded to the teeth with an indirect bonding resin. In group 2, before bonding, an antimicrobial varnish was painted on the etched enamel and indirect bonding was carried out as in group 1. In group 3, Transbond MIP primer and the antimicrobial varnish were thoroughly mixed in a 1:2 proportion, applied to the enamel surface, light cured for 20 seconds, and the brackets were direct bonded. A universal testing machine was used to determine the maximum load necessary to debond the brackets, the SBS values recorded, and the adhesive remnant index scores determined. Data were analyzed using analysis of variance (ANOVA), Tukey HSD, and chi-square tests. Results of ANOVA revealed statistically significant differences in the SBS among the various groups tested (P < .05). Indirect bonding of brackets with Sondhi Rapid Set after the application of the antimicrobial varnish showed significantly lower SBS when compared with both the group 2, indirect bonding control group, and the group 3, direct bonded-antimicrobial varnish group.