Gene deletion and hybrid gene formation result in congenital red and green color vision defects. The innumerable variations in these defects require the development of appropriate methods for detailed investigation. We used heteroduplex-single-strand conformation polymorphism (SSCP) analysis to detect the gene variations in subjects with congenital red and green color vision defects. For comparison, we also used polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) to detect these defects. In all 13 protan and 9 of the 15 deutan subjects, defects of the red or green pigment gene could be identified by either heteroduplex-SSCP or PCR-RFLP analysis. Through heteroduplex-SSCP analysis, sequence polymorphism was detected in exon 5 of the green pigment gene. One polymorphic sequence was present in 8 of 21 trichromats but in only one of 17 dichromats, showing a biased distribution. A specific variation was found in one protan by SSCP analysis. Heteroduplex-SSCP procedures are useful for objective clinical diagnostic testing and for further study of color vision variations because of their simplicity and reliability and because they provide more information.