Cryptorchidism, or retained testicles, is one of the most common congenital developmental defects in purebred dogs. DNA markers called single nucleotide polymorphisms (SNPs) are being used to investigate the associations between 21 candidate genes and cryptorchidism in Siberian huskies. We found the genes COL2A1, HOXA10, INSL3 and TIMP1 tended to be associated with cryptorchidism in Siberian huskies. The results will help to find the causative mutations in the future and will be useful in dog breeding programs to reduce the incidence of cryptorchidism.