With the objective of studying and protecting genomes of autochthonous breeds of cattle, investigations were performed of the variability of morphometric characteristics of the autochthonous breeds Busa and Gatacko cattle, as well as a retrospective analysis of the development of the examined populations. The investigations covered 97 cows, specifically 22 head of western Herzegovina Busa cattle, 24 head of eastern Herzegovina Busa cattle, and 51 head of Gatacko cattle. Morphometric measurements were examined: height at withers, body length, foot circumference, and chest girth. The obtained data were processed statistically, and variability was established using simple variance analysis with an unequal number of repetitions. The significance of the obtained differences from the three investigated localities was tested using the F test and t-test. A significant degree of variability was established for the morphological characteristics within the examined populations, as well as between the populations. The established differences are primarily a result of the influence of different natural conditions and breeding conditions, as well as the genome share of Alpine cattle, with which the Busa has been crossbred.