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Hemimelia is a common congenital limb abnormality found in water buffaloes from Southern Italy. In humans, such defect has been associated with mutations in WNT7A and ESCO2 genes. These two candidate genes were analyzed by polymerase chain reaction in the genomic DNA extracted from the blood of buffaloes, and cows for control. No differences in WNT7A and ESCO2 sequences between affected and healthy buffaloes were identified. However, comparing sequences of control cows and buffaloes, WNT7A showed simple species polymorphisms, and ESCO2 showed seven base-pair substitutions. These results demonstrate that limb malformations in buffaloes are not related to congenital defects in WNT7A gene. Interestingly, our findings highlight for the first time differences in the sequences of WNT7A and ESCO2 genes between buffaloes and cows.