Using polymerase chain reaction-based microsatellite analysis we examined 40 cases, tumor biopsies and cytological material, of early stage cervical cancer and 20 healthy donors. Loss of heterozygosity (LOH) was detected in 35 out of 40 cases (87.5%), located on 9pter-p13 (67.5%), 9q32-34 (17.5%), 13q12 (32.5%), 17p13 (0%) and 17q11-q22 (12.5%). Microsatellite instability (MIN) phenotype was found in three out of 40 cases (7.5%). The accuracy in LOH and MIN detection in cytological material compared to tumor biopsies was 91.5 and 86.0%, respectively. None of the specimens of healthy donors exhibited any genetic alteration. Our data suggest that microsatellite analysis in cytological material could be used for the early detection of cervical cancer.