Many cellular functions including gene expression and chromosome structure are highly dependent upon the precise recognition and binding of specific DNA elements by regulatory and structural proteins. DNA damage that alters protein/DNA interactions therefore has the potential to disrupt normal cellular functions including proliferation. As a model to examine the interaction of proteins with damaged DNA, the binding of AP-1 transcription factor to cognate DNA elements with 8-oxoadenine, 8-oxoguanine and abasic sites was studied by gel mobility shift analysis. Of the three types of DNA damage only 8-oxoadenine was without effect on AP-1 binding. A single 8-oxoguanine could partially inhibit AP-1 binding when located at specific positions within and even adjacent to the conserved AP-1 binding sequence. Abasic site damage also demonstrated a position effect but with more overall inhibition. When 8-oxoguanine and abasic sites were combined to model the multiple damage sites produced by ionizing radiation there was a cumulative loss of AP-1 binding that appeared to be synergistic. These results suggest protein/DNA interactions can be quite sensitive to the site, degree, and type of DNA damage, even relatively minor modifications.