We have previously described an allelic variant of the human H2R, nominated the H2R649G allele. This allele contains an adenine-->guanidine substitution at base 649, which introduces an additional TaqI restriction endonuclease site into the gene. With this in mind, we have investigated allelic polymorphism of this receptor and its association with schizophrenia. H2R DNA from 47 schizophrenic patients and 46 control subjects was amplified by the polymerase chain reaction (PCR). These PCR products were analyzed by observing TaqI cleavage patterns and single-stranded conformational polymorphisms. It was found that the H2R649G allele was 1.8 times more frequent in the schizophrenic population (chi 2 test P < 0.01). In addition, schizophrenic individuals were 2.8 times more likely to be homozygous for the H2R649G allele than the control population, (chi 2 test P < 0.05). These data place the attributable fraction for possession of the H2R649G allele at 28.4%.