Insulator protein ZIPIC of Drosophila melanogaster is capable of specific binding to DNA. Previously, zinc finger motifs at the C-terminus of the protein have been shown to interact with DNA. ZIPIC can bind to CAGGGCTG sequence. In the present work the interaction of ZIPIC with two minor binding sites, CAGTGGCTG and CAGGGATG, has been examined. ZIPIC showed weak interaction with the first binding-site variant, which has G-to-T substitution in the 4-position, and is only observed in vivo; it can be attributed to the presence of additional transcription factors that facilitate the binding of the protein. The other binding site variant, which has C-to-A substitution in the 6-position, interacted with ZIPIC effectively in vitro, but not in vivo. This suggests the existence of an unknown transcription factor that binds to this variant more effectively than ZIPIC.