Oncogenic human papilloma viruses (mostly HPV types 16 and 18) are the major cause of cervical intraepithelial neoplasia (CIN) that progress into cervical cancer (CC). To reveal early genetic alterations at chromosome 6 important for CC progression we have analyzed loss of heterozygosity (LOH) in DNA from 45 CIN cases, 47 microcarcinomas and 19 invasive squamous cell carcinomas stage IB. LOH analysis of DNA samples prepared with microdissection from all CIN foci as well as from CC lesions and synchronous CIN has permitted the investigation of CIN and CC heterogeneity. 79% of CC stage 1 showed LOH with 6 microsatellite markers at chromosome 6. LOH with microsatellite markers D6S276 (6p22) and TNFalpha (6p21.3) was found in 50% of CC cases. LOH frequency in CIN lesions, synchronous with CC, was higher then LOH in CIN cases without cancer, the statistical significance (p = 0.004) was shown for marker D6S291 (6p21.2). The finding suggests that high level of LOH frequency in CIN lesions may be a marker of unfavorable prognosis for CIN. Progression from microcarcinoma to invasive CC of IB stage was associated with higher LOH frequency at D6S344 (6p25) and TNFalpha (6p21.3). The early genetic alterations were found in CIN with microsatellites D6S273 and TNFalpha located at 6p21.3. Moreover the LOH frequency at D6S273 retained the same in CIN and CC cases. Based on HPV-typing, LOH analysis and X-chromosome inactivation the polyclonality of CC lesions as well as CIN was shown in a few patients.