Pax-6 genes, known to be essential for eye development, encode an evolutionarily conserved transcription factor with two DNA-binding domains. To corroborate the contribution of each DNA-binding domain to eye formation, we generated truncated forms of the Drosophila Pax-6 gene eyeless and tested their capacity to rescue the ey(2) mutant. Surprisingly, EY deleted of the homeodomain rescued the ey(2) mutant and triggered ectopic eyes morphogenesis. In contrast, EY lacking the paired domain failed to rescue the ey(2) mutant, led to truncation of appendages, and repressed Distal-less when misexpressed. This result suggests distinct functions mediated differentially by the two DNA-binding domains of eyeless.