Base excision repair (BER) is a key pathway for maintaining genomic stability. A key enzyme in the BER pathway is DNA polymerase beta (polbeta). It has been shown that more than 11% of breast, bladder, esophageal, colon, and gastric cancer samples studied so far exhibit polbeta mutation. A truncated form of polbeta, polbetadelta (exon 11 deletion), identified in a colon tumour sample, exhibited dominant negative activity. Using this polbetadelta as bait, we screened a HeLa cDNA library for any interacting protein(s) in the yeast two-hybrid (Y2H) system. Polbetadelta was cloned into a pGBKT7 vector (pGBKT7-polbetadelta). pGBKT7-polbetadelta was transformed into the yeast strain AH109. Then the cDNA library was co-transformed into AH109/pGBKT7-polbetadelta and screened by the selection procedure. The yeast-purified plasmids were transformed into Escherichia coli. Plasmid DNA was isolated from the colonies, purified, digested with Sma I and Sal I, and the fragments were sequenced. Four positive clones were obtained. Out of these, three proteins were already known to interact with polbeta (XRCC1, MGC5306, and AP endonuclease 1). The only member previously not known to interact with polbeta was phosphatidylinositol glycosylase type S (PIGS). PIGS is a 64-kDa membrane protein, encoded in chromosome 17. The PIGS protein interacts also with wild-type polbeta which was confirmed by co-immunoprecipitation and Western blot analysis. The role of the newly identified protein in the dominant negative function of the variant form of polbeta remains to be seen.