The study includes a survey undertaken in Burundi, Rwanda, Tanzania & Uganda describing production systems & selection criteria; a novel approach of phenotypic ranking for the evaluation indigenous selection criteria and assessing regional differences in morphology and genotype of the Ankole cattle to provide information on genetic variation of the breed and thus breeding goals. The survey shows that in Burundi, Rwanda and the SW highlands of Uganda, cattle keepers are entirely sedentary and own small herds while elsewhere they are sedentary / semi- nomadic. Milk is the main product in all areas. The selection criteria for cows are similar across systems. Production traits were highly ranked including growth for bulls. Phenotypic appearance and ancestral information are more important in bulls than in cows. In areas of land scarcity there is tendency toward crossbreeding. From the phenotypic ranking experiments cattle keepers preferred cows of good production traits while in bulls, the criterion of appearance is crucial. Own fertility followed by milk performance are the main criteria for selecting cows, resistance to East Coast Fever was of highest importance in bulls. Genetic & morphological characterisation of Ankole cattle was done in Burundi, Rwanda, Tanzania Uganda and the DR Congo. The traits of largest variation proportion attributed to region were femoral thigh length, horn length, horn base circumference, rump height, body length and height at withers. 2.7% of the genetic variation is attributable to differences among sub-populations. Four genetic structures were inferred from a model based Bayesian approach. Both the latter & distance based analyses consistently isolated the Mugamba sub-population in Burundi from the rest.