In the preceding paper [M. Wojewodzka, M. Kruszewski, T. Iwanenko, A.R. Collins, I. Szumiel, Application of the comet assay for monitoring DNA damage in workers exposed to chronic low dose irradiation. I. Strand breakage., Mutat. Res. 416 (1998) 21-35], we reported the results of DNA damage examination carried out for a group of people (49 individuals) professionally at risk of exposure to low doses of ionizing radiation as measured by the alkaline comet assay. Here, we used the method in combination with oxidative base damage-specific endonucleases to estimate base damage in the same individuals. These were endonuclease III (endoIII) and formamidopyrimidine glycosylase (FPG). In contrast to the previous investigations, we found no statistically significant difference in base damage between the control and hazard groups. Interestingly, the hazard group exhibited lower level of enzyme-sensitive sites than the control; however, this different was not significant. No correlation of base damage with age was found, similarly as in the case of DNA damage measured by the alkaline comet assay. Interindividual variability of base damage precluded exposure estimation for single individuals, since several members of the control group exhibited high comet parameters.