Genetic factors could affect the incidence of scrotal hernia in pigs. To detect genomic regions or genes involved in the development of scrotal hernia, we genotyped 12 affected and 12 control inbred animals using the Porcine 60K Beadchip. After case-control association analyses, using both single marker and Bayesian analyses, we confirmed the involvement of genomic regions on SSC2, SSC5 and SSCX. Homozygosity mapping was also used to detect several possible recessive regions. Given previous reports implicating SSC2 in most studies we selected two candidate genes on SSC2, CTNNA1 and Testican1, and discovered synonymous SNPs in exonic regions and 3’-untraslated regions. However, no apparent causative mutations were found. Further investigation on the structural variation and functional importance of these genes and regions is still needed.