The relationship between molecular structure of the visual pigment genes and red-green color vision was studied in 126 normal and 63 color-defective males. We found that the great majority of defects in red-green color vision are associated with the formation of 5′R-G hybrid genes (protan series), deletion of the G gene (deutan series), or the formation of 5′R-G hybrid genes (deutan series). Within these two series, however, dichromacy and trichromacy cannot always be predicted from the molecular patterns, particularly among protans. Amino acid residues in exon 5 largely determine whether a hybrid gene will be more R-like or more G-like in phenotype. We observed numerous genetic polymorphisms in the R and G pigment genes of both normal and color-defective subjects. These polymorphisms may account for some, but not all, of the observed variations in color vision phenotypes. A common Ser/Ala polymorphism at position 180 of the R pigment gene was found to be highly correlated with the bimodal distribution of Raleigh matches we observed among 50 color-normal Caucasian males.