Abstract. This study was performed to examine the distribution of single nucleotide polymorphisms (SNPs) and estimated haplotypes in the canine estrogen receptor (ER) α gene (ESR1) and the association of them with different phenotypes of cryptorchidism (CO) in Miniature Dachshunds and Chihuahuas. Forty CO and 68 normal dogs were used, and CO was classified into unilateral (UCO; n=33) and bilateral CO (BCO; n=5) or into abdominal (ACO; n=16) and inguinal CO (ICO; n=22). Thirteen DNA fragments located in the 70-kb region at the 3' end of ESR1 were amplified by PCR and sequenced to examine 13 SNPs (#1-#13) reported in a canine SNP database. Ten SNPs (#1-#4, #7, #8, #10-#13) were not polymorphic, and 5 new SNPs (#14-#18) were discovered. A common haplotype block in normal, CO and CO phenotypes was identified for an approximately 20-kb region encompassing 4 SNPs (#14-#17). Allele, genotype and haplotype frequencies in CO without classification by phenotype and also in UCO, ACO and ICO phenotypes were not statistically different from the normal group. Significant differences in genotype frequencies and homozygosity for the estimated GTTG haplotype within the block were observed in BCO compared with the normal group, although the number of BCO animals was small. Our results demonstrate that the examined SNPs and haplotypes in the 3' end of canine ESR1 are not associated with unilateral, abdominal and inguinal CO phenotypes and CO per se in Miniature Dachshunds and Chihuahuas. Further studies are necessary to suggest a clear association between the ESR1 SNPs and bilateral CO in dogs. Key words: Cryptorchidism, Dogs, ESR1, Haplotype, Single nucleotide polymorphisms (SNP) (J. Reprod. Dev. 56: [405][406][407][408][409][410] 2010) ryptorchidism (CO) is a developmental defect in male dogs in which descent of one or both testes into the scrotum does not occur by 6 months of age [1]. CO is believed to be heritable [1,2], and the findings of a recent study [3] using carrier and non-carrier parents and their litters in dogs are also supportive of this phenomenon. Clinically, CO manifests in different phenotypes, including unilateral-or bilateral-retention cases and abdominal-or inguinalretention cases. However, the causative or associated genes of canine CO and CO phenotypes are unknown. Except for penilepreputial defects [4], the association between other congenital reproductive diseases and CO has not yet been reported. The incidences of cryptorchidism reported in previous studies of various breeds of dogs range from 1.2 to 10.7 percent [5][6][7][8]. The incidence of cryptorchidism is higher in smaller breeds compared with larger breeds [9].In humans, several candidate genes including androgen receptor (AR) gene [10][11][12], estrogen receptor (ER) gene [13][14][15], insulinlike peptide 3 (INSL3) gene and INSL3 receptor (LGR8) gene [12,[16][17][18] have been investigated for CO. Using single nucleotide polymorphism (SNP) genotyping, which is one of the recent molecular approaches applied to identify candidate genes [19], Yo...