The frequencies of spontaneous and in vitro mutagen-induced unstable chromosomal lesions were compared in the groups of subfertile cows, ewes and sows (test groups) as well as the animals without any reproductive disturbances (control groups). The mean percentage of 5-azacytidine- and bromodeoxyuridine-induced defects differed statistically between the test and control groups (P≤0.01 in cattle, P≤0.05 in sheep and pigs). In the groups of animals with reproductive problems the number of defects observed in some chromosomes exceeded the expected values (calculated according to the relative chromosome length), but only in the case of X chromosome differed at the level of statistical significance. Moreover, the groups of cows analysed differed significantly as regards the number of chromatid breaks/gaps at the Xq2.4 and Xq3.1 fragile sites. The excessive chromosome instability in subfertile farm animals, particularly the X-specific loci, may result in inappropriate expression of genes determining reproductive traits as well as in the increased rate of aneuploid germ cells related to prenatal and perinatal mortality.