Auto-antibodies against topoisomerase I (topo I) are frequently detected in sera of systemic sclerosis (SSc) patients. Anti-topo I auto-antibodies are considered to be associated with the diffuse cutaneous form of systemic sclerosis (dcSSc). However, anti-topo I auto-antibodies are also detected in limited cutaneous systemic sclerosis (lcSSc) and systemic lupus erythematosus (SLE). In this study, we compared the epitope specificity of anti-topo I auto-antibodies present in sera of dcSSc, lcSSc and SLE patients. We have constructed an antigen fragment library displayed on bacteriophage lambda and screened this library with IgG purified from patients' sera. Regions of topo I selected from the library were expressed as recombinant fusion proteins and were tested with ELISA and western blot. We unexpectedly found that antibodies against a fragment of topo I [fragment F4 [amino acid (AA)] 451-593] could be detected in sera of healthy individuals and patients with inflammatory rheumatic diseases other than SSc and SLE. Using sera of dcSSc, lcSSc and SLE patients, we showed that the pattern of recognized epitopes is different between these patient groups. Fragment F4 was recognized by all patients. Fragment F1 (AA 5-30) was recognized by 9 of 34 dcSSc patients. Fragment F8 (AA 350-400) was recognized by four of eight SLE patients. Analysis of clinical data revealed a significant difference between the F1-negative and F1-positive groups of SSc patients in age and in the duration of the disease. According to our results, the newly identified fragments F1 and F8 could represent characteristic epitopes for dcSSc and SLE, respectively.