Following domestication, man selected the horse primarily for the purpose of transportation rather than consumption; this selective strategy created divergent traits for locomotion. At intermediate speeds, beyond the flat walk, the horse can perform a range of diagonal and lateral 2-beat or 4-beat gait patterns. The Tennessee Walking Horse (TWH) is the only U.S. breed able to perform an even-timed 4-beat gait (the "running-walk") at intermediate speeds; however, within the breed, there is remaining variation in gait type. To investigate the contribution of genetics to this unique trait, blood or hair samples for DNA and gait information were collected from 129 TWH and genotyping was performed at approximately 60,000 loci using the Illumina Equine SNP70 beadchip at GeneSeek Inc. (Lincoln, NE). Case-control association tests identified suggestive regions for gait type on equine chromosome (ECA) 19 (-value of 1.50 x 10(-5) after 1 million permutations; PLINK version 1.07). Haplotype analysis identified 2 significant haplotypes on ECA19 and ECA11 (-values of 3.7 x 10(-5) and 3.92 x 10(-5), respectively). Genes within these suggestive regions play roles in developmental processes and biological regulation, indicating there may be variant differences in the neurobiology and regulation of horses with a polymorphic gait.