Aneuploidy is associated with spontaneous abortions, perinatal mortality, mental retardation and with embryonic and foetal mortality. Most of these abnormalities originate as a result of meiosis errors during gametogenesis. The main purpose of the study was to analyse frequency of aneuploidies of sex chromosomes and chromosome 6 by three-colour fluorescence in situ hybridization (FISH) in 47 young bulls, candidates for artificial insemination programme with cryopreserved semen and to investigate the influence of aneuploidies and disturbed sperm chromatin integrity on non-return rates, the frequencies of abortions, perinatal mortality and stillbirths. The average frequencies of spermatozoa with disomy for chromosomes X, Y, XY and 6 were 0.032, 0.005, 0.003 and 0.039% respectively. The incidence of XX66, YY66 and XY66 diploidy was 0.017, 0.006 and 0.015% respectively. Frequencies of meiotic II errors were significantly higher than meiotic I errors (p < 0.01). More X bearing spermatozoa than Y bearing spermatozoa were detected (5151 vs. 5022; p < 0.01). Sperm chromatin damage expressed by DNA fragmentation index (DFI) was 5.3 +/- 3.7 and percentage of cells with defective chromatin condensation (HDS) was 1.4 +/- 0.8. No correlation was found between sperm aneuploidy and basic sperm analysis. The relationship was found between non-return rate and total aneuploidy (r = -0.310; p = 0.036). Significant correlation was found between sex disomy, total aneuploidy (disomy of chromosomes 6, X, Y and XY spermatozoa and diploidy) and stillbirths (r = 0.390; p = 0.013; and r = 0.331; p = 0.037). Chromosome 6 disomy correlated with perinatal mortality (r = 0.317; p = 0.047). HDS correlated significantly with total aneuploidy (r = 0.449; p = 0.002). Our study indicated that aneuploidy frequencies in young fertile bull spermatozoa are relatively low. Nevertheless, there exists a variability in aneuploidy frequencies amongst bulls, which appears to be able to have an influence on the fertility of these animals.