The development of the first SNP array (Affymetrix Axiom Buffalo Genotyping Array) officially opened the genomic era for the Buffalo species. More than 123k SNP probes are currently available for the genotyping of 90k SNPs. A total of 1605 individuals were genotyped worldwide within the framework of the International Buffalo Genome Consortium (1376 River Buffalo, 200 Swamp Buffalo, 15 Cape Buffalo, 14 Anoa) which were used to assess the performance of the chip. An automated open-source pipeline, ???AffyPipe???, was created to analyze Affymetrix Axiom data of any species in a Linux/MacOS environment. The pipeline streamlines the Affymetrix software and allows a much more user-friendly, simple and flexible extraction of genotypes than the standard Affymetrix protocol. The results obtained showed a very good overall performance of the Buffalo SNP array, with expected differences in terms of polymorphic SNP across populations. However, problems with some SNP probes, which gave inconsistent information, were seen. These minor inconsistencies do not hamper the overall performance of the Buffalo Axiom SNP array. Recommendations for the correct use of the Buffalo array will be presented.