Recent advancements in molecular biology have revealed genetic aspects of congenital color vision deficiencies (CVD). In many cases of CVD, the genotypes and phenotypes coincide with each other But it is also known that there are cases in which the genotype alone cannot explain the clinical diagnosis of CVD. So it is still unclear whether routine gene analysis is useful as a clinical diagnostic tool for this anomaly. We evaluated the clinical usefulness of genetic analysis for congenital red-green color-vision deficiencies. The nucleotide sequences of red-green pigment genes of 62 CVD cases and 113 color-normal males were determined using PCR and a DNA sequencer (ABI PRISM 310 Genetic Analyzer). The CVD cases were diagnosed using clinical color-vision tests including an anomaloscope. The color-normal subjects were tested with Ishihara plates and if needed, with an anomaloscope. All normals had two types of exon 5, i.e., both red and green pigment genes. Forty-seven (76%) of 62 CVD cases had genotypes that coincided with their phenotypes. Three dichromats (one protanope and two deuteranopes) had genetic potential to be anomalous trichromats, Twelve deutans (one deuteranope and 11 deuteranomals) could not be differentiated from the normals: they had both red and green types of genes, as did the normals. All in all, 15 cases (24%) had some inconsistencies between the phenotype and the genotype. Pigment gene analysis alone could not fully differentiate CVD from normals. (C) 2000 John Wiley & Sons, Inc. Col Res Appl, 26, S89-S92, 2001.