To preserve endangered cattle breeds, pedigree analysis is a good method to analyse genetic structure in order to predict the evolution of genetic variability. This study investigated the pedigrees of three highly endangered local cattle breeds of Austria: Pustertal Spotted Cattle, Ennstal Pied Cattle and Original Austrian Brown Cattle. Pedigree files are included from 22,451 animals in Original Austrian Brown Cattle to 1,327 animals in Ennstal Pied Cattle. Breeders follow the conservation programme of ÖNGENE (Austrian Association for Rare Endangered Breeds) by systematically avoiding mating of closely related animals, applying the projected inbreeding coefficient of the potential progeny as indicator. Three reference populations were defined: 1) living population; 2) male living animals of which no semen was available; 3) bulls for which semen was available. PEDIG software was used to calculate genetic parameters in order to evaluate the genetic variability. The significance of the results strongly depends on the quality of the pedigrees. While Original Austrian Brown is derived from a large ancestral population, the two other breeds are based on very small numbers of founder animals. The inbreeding coefficient is less than 1% for Original Austrian Brown Cattle and Pustertal Spotted Cattle. In contrast, the Ennstal Pied Cattle has a percentage of 3.3%. In all three breeds the effective number of founders is unequal to the total number of founders, which implies an unbalanced use of founders. When increase of inbreeding coefficients from the parents of the current population to the current population was calculated, effective population sizes were 238 for Original Austrian Brown Cattle, 82 for Pustertal Spotted Cattle and 34 for Ennstal Pied Cattle. In terms of important ancestors, of the 20 most important ancestors of the living Ennstal Pied Cattle population are mostly female (17) and date back to the seventies. For other two breeds the majority of the most important ancestors are male (18 for Original Austrian Brown Cattle and 13 for Pustertal Spotted Cattle) and for Original Austrian Brown Cattle the bulls date back to the nineteen-fifties. This study confirmed that in small cattle populations special mating programmes and conservation programmes are needed in order to minimize the loss of genetic diversity.