The prevalence of undermasculinized external genitalia has increased in several countries including Japan, and this phenomenon has primarily been ascribed to the deleterious effects of environmental endocrine disruptors such as dioxins. To examine a possible role of the genetic susceptibility to dioxins in the development of micropenis (MP), we studied the Arg554Lys polymorphism of the gene for aryl hydrocarbon receptor (AHR) and the Pro185Ala polymorphism of the gene for aryl hydrocarbon receptor repressor (AHRR), in 73 boys with MP (34 boys with mild MP from –2.1 to –2.5 SD and 39 boys with severe MP below –2.5 SD) and 80 control males (50 boys and 30 fertile adult males). The allele and genotype frequencies of the AHR polymorphism were comparable between the two groups of males, but those of the AHRR polymorphism were significantly different, with the Pro allele and the Pro/Pro genotype being more frequent in boys with MP than in control males (P-value: 0.0029 for the allele frequency and 0.011 for the genotype frequency). In addition, both polymorphisms were comparable in the allele and genotype frequencies between boys with mild MP and those with severe MP and between control boys and control fertile adult males. The results suggest that the AHRR Pro185Ala polymorphism may constitute a susceptibility locus for the development of MP in response to dioxins.