A genetic association between schizophrenia and a silent C/T(102) polymorphism in the 5-HT2A receptor gene (5-HT2AR) has been previously reported; however, the mechanisms underlying this association remain unknown. Here we developed an improved quantitative assay for measurements of allele ratios, which revealed that the expression of allele "C" in the temporal cortex of normal heterozygous individuals was significantly lower than the expression of allele "T" (allele "C" to allele "T" ratio of approximately 0.8, P < 0.0001). Confirming decreased expression of allele "C," total levels of 5-HT2AR mRNA and protein in normal individuals with the C/C genotype were lower than in individuals with the T/T genotype. Similarly to normal individuals, allele "C" to allele "T" ratio in heterozygous schizophrenics was reduced (approximately 0.8, P < 0001). This ratio was independent of neuroleptic treatment history. By contrast, total levels of 5-HT2AR mRNA correlated inversely with neuroleptic free interval prior to death (r = -0.67, P < 0.001) suggesting a reversible neuroleptic effect. Total levels 5-HT2AR mRNA in neuroleptic free (> 26 weeks) schizophrenics (n = 11) were significantly lower than in controls (P = 0.03). The data suggest that increased prevalence of allele "C" among schizophrenics may be due to intrinsically low expression of this allele, which may contribute to a deficit in 5-HT2AR expression in some schizophrenics.