A cohort of 70 consecutive women at a university hospital colposcopy clinic with untreated CIN I and CIN II (CIN I/II) confirmed by cytology and histology was followed for 1 year in the setting of a prospective trial. In the lesions, the presence of DNA from HPV types was examined by restriction fragment length polymorphism (RFLP) analysis. Aneuploid cell lines were demonstrated by aneuploid histograms generated by high-resolution DNA flow cytometry. HPV type 16 infection and the existence of aneuploid cell lines proved to be significant risk factors for CIN I/II lesions to persist or progress to CIN III in the 1-year follow-up period in the same cohort of patients. The relative risks and 95% confidence intervals (CI) were 1.81 (1.44-2.76) for aneuploid cell lines and 1.74 (1.10-2.76) for HPV type 16 infection in CIN I/II lesions. As a predictive diagnostic test for CIN I/II lesions to persist or progress, the specificity and positive predictive value (PPV) for aneuploid histograms were 100% (CI, 73.5-100%) and 100% (CI, 86.8-100%), respectively. The low sensitivity of 27.3% (CI, 14.9-42.8%) restricted the clinical application of the test, leaving 32 of 44 women with persisting or progressing CINI/II with diploid histograms. HPV type 16 positivity by FRLP had a PPV of 68.4% (CI, 43.5-87.4%) as a prognostic test. Six of 19 HPV 16 infected women showed complete remission of their CIN lesion. A combination of the two tests did not provide any additional information.