Using ligation-mediated polymerase chain reaction to separately map the distribution of induced oxidized bases and strand breaks along the human PGK1 promoter at nucleotide resolution, we previously described the pattern of oxidative DNA damage induced in vitro by Cu(II)/ascorbate/H2O2 [J. Biol. Chem. 270, 17633-17640 (1995)]. Here we report that the pattern of in vivo base damage caused by H2O2 is almost identical to that of the previously used in vitro system with the exception of transcription factor-associated footprints. An unusually strong positive footprint for both strand breaks and oxidized bases is associated with binding of the hypoxia-inducible transcription factor-1. Base damage at this footprint was 52-91% repaired in 24 h, which was similar to the global base damage repair rate. However, strand breaks at this footprint were only 39-55% repaired in 24 h or approximately 100-fold slower than the global strand break repair rate.