We found 26 bovine genomic regions in European and African Bos taurus carrying distinctive signatures of selection. Of these, 12 (46%) contained 30 stature-associated candidate genes derived from comparative mapping. We showed that when cohorts of randomly permuted animals were tested, a much lower proportion (8.3%) of the significant regions contained candidate genes, which is consistent with random expectations (∼7%). This suggests that our approach was powerful in capturing bovine genomic regions related to stature. Several of these should be considered novel because they were not previously reported in cattle.