The objective of this study was to determine microsatellite polymorphism in Rhode Island Red (RIR) and Sussex (SX) chickens, divergently selected over six generations for high (H) or low (L) incidence of skeletal defects in embryos (30.7% for H lines, 3.7% for L lines). The polymorphism analysis covered 15 microsatellite markers within four lines (a total of 60 individuals). Eight alleles were identified as specific to H lines and six alleles as specific to L lines. The selection for skeletal malformation appears to have affected the frequency of microsatellite alleles. The experimental material examined constitutes a valuable source for identification of real genes causing skeletal defects.