Bleomycin is a well-established anti-tumor drug. Its major untoward effect, pulmonary toxicity, has limited its usage. In this study, we used a DNA repair protein, yeast apurinic/apyrimidinic endonuclease (APN1) to reduce the toxicity of bleomycin on lung cells. A549 cells, an alveolar epithelial cell line, were transduced by MIEG3 retroviral vector encoding both enhanced green fluorescent protein (EGFP) and APN1. Transduced cells were sorted by fluorescent-activated cell sorter (FACS) analysis and were cloned. The APN1 expression of transduced A549 cell population and four selected clones expressing different levels of EGFP was confirmed by Northern, Western, and apurinic/apyrimidinic (AP) endonuclease activity analyses. The expression of APN1 was positively correlated with the expression of EGFP. The protective effect of APN1 against bleomycin was determined by single cell gel electrophoresis/Comet assay and by clonogenic survival assay following bleomycin treatment. The A549 population expressing APN1 showed a significant reduction of DNA damage in the presence of 20, 50, and 100 microg/ml bleomycin; similarly, the APN1-expressing A549 population also demonstrated increased survival in the presence of bleomycin compared with the vector-transduced A549 population. In selected clones, three of four APN1-expressing clones resulted in significantly improved cell survival. The current study suggests that the yeast DNA repair protein, APN1, can reduce bleomycin toxicity to target lung cells.