Cryptorchidism (CO) as a common developmental defect in purebred dogs causes health concerns of reduced fertility and increases risk of testicular malignancies. A total of 49 single nucleotide polymorphisms (SNPs) discovered from 20 candidate genes was investigated to analyse their associations with CO in Siberian Huskies. The sibling-transmission disequilibrium test on 38 discordant full-sibs revealed seven SNPs in the collagen type II alpha 1 (COL2A1) gene were significantly (p < 0.05) or suggestively (p < 0.10) associated with CO. Further analyses showed that only one SNP (rs23358342) in this gene remained suggestively significant (p < 0.1) on a data set of full-sibs with additional related dogs, but not significant on all 156 Siberian Huskies. Based on the statistical results and the involvement of COL2A1 in the testicle development and descent, we could not exclude COL2A1 as a potential candidate gene for CO in Siberian Huskies. Further studies are necessary to clarify these results from our relatively small sample size.