In a recent study we confirmed that QTL regions on pig chromosomes 11, 13, and 15 are associated with reproduction traits in the pig. Within these regions the genetic variation was largest on chromosome 13. The QTL region on this chromosome was therefore studied further to identify genes known to contribute to litter size. The superoxide dismutase (SOD1) gene localized at around 200 Mb in the pig (Sscrofa10) was the most obvious candidate gene. In the present study, we have cloned and sequenced the porcine SOD1 gene. The SOD1 amino acid sequence is highly conserved between human, mouse, rat, and pig. Expression studies by quantitative PCR showed differential levels of the SOD1 transcript in all tissues investigated. Sequence comparison between sows with high and low estimated breeding value (EBV) for litter size, revealed a total of eight single nucleotide polymorphisms (SNPs) in the noncoding sequence and no SNPs in the coding region. One of the intronic SNPs was genotyped in 248 sows with high and low EBV for litter size. Allele frequency differed significantly between the two group of sows indicating that polymorphism in the chromosome 13 locus has an impact on litter size. The sows homozygous for the A/A genotype conceive three piglets more compared to the A/T genotype, making this SNP a possible marker for litter size. However, this genotype was negatively correlated with other important traits under selection in the Danish pig production.