Genetic polymorphisms in DNA repair genes can affect the risk of developing different forms of cancer. Therefore, we have studied the putative association of seven single nucleotide polymorphisms (SNPs) in five DNA repair genes with the incidence of chronic lymphocytic leukemia (CLL). We included 461 CLL patients and the same number of age- and sex-matched controls. As chromosomal aberrations are important prognostic markers in CLL, we additionally correlated the SNPs with the occurrence of favorable and unfavorable cytogenetic aberrations in CLL patients. Patients with del(13q) as a sole aberration were allocated to the favorable cytogenetic risk group, and patients with del(17p) and/or del(11q) to the unfavorable cytogenetic risk group. All investigated SNPs were equally distributed between patients with the favorable cytogenetic aberration and controls. However, differences were observed in the distribution of rs13181 in ERCC2 between all CLL patients and controls. Moreover, the clearest differences were found for rs13181 in ERCC2 and rs25487 in XRCC1 between CLL patients with unfavorable cytogenetic aberrations and controls. These data suggest that inborn genetic polymorphisms may predict the outcome of CLL.