Cryptorchidism, or retained testicles, is one of the most common congenital developmental defects in purebred dogs. A genome wide association study (GWAS) was performed using the CanineHD BeadChip. Genotyping data was analyzed by case-control analysis in PLINK software and the BayesB approach in GenSel software with the genome partitioned into 1Mb windows of SNPs or haplotypes. No significant association was observed in the case-control analyses after corrections for False Discovery Rate (FDR) in PLINK. In contrast, the BayesB analysis identified a 1Mb region on dog chromosome 27 (CFA27) containing the AMHR2 (anti-mullerian hormone type II receptor) gene that explained a high percentage of genetic variance. In conclusion, we identified a putative candidate region at the 4^th Mb on CFA27 (CanFam2.0) harboring a very promising functional candidate gene AMHR2associated with the development of cryptorchidism in our Siberian Husky population.