While the negative effects of inbreeding and reduced heterozygosity on fecundity and survival are well established, only a few investigations have been carried out concerning their influence on morphological traits. This topic is of particular interest for a small and closed population such as the Lipizzan horse. Thus, 27 morphological traits were measured in 360 Lipizzan mares and were regressed on the individual inbreeding coefficients, as well as on the individual heterozygosity and mean squared distances (mean d(2)) between microsatellite alleles within an individual. Both individual heterozygosity and mean d(2) were based on 17 microsatellite loci dispersed over 14 chromosomes. The results obtained by multivariate analysis reveal significant effects of stud (P <.0001), age at measurement (P <.0001), and mean d(2) (P =.0143). In univariate analyses, significant associations were obtained between length of pastern-hindlimbs and inbreeding coefficient (P <.01), length of cannons-hindlimb and mean d(2) (P <.01), and length of neck and mean d(2) (P <.001). After adjustment of single-test P values for multiple tests (Hochberg"s step-up Bonferroni method), only the association of the length of neck and mean d(2) remained significant (P =.0213). Thus, no overall large effects of inbreeding, microsatellite heterozygosity, and mean d(2) on morphological traits were observed in the Lipizzan horse.