The etiology of chronic lymphocytic leukemia (CLL) appears to be influenced by genetic factors which may contribute to its differential, gender- and age-specific incidence. The presented study is the first, which investigated the frequencies of DNA-typed alleles of all relevant human leukocyte antigens (HLA) loci in CLL patients with regard to gender and age at disease onset. The most remarkable result was the higher frequency of homozygosity for MHC class II loci in female patients. Particularly, an increased frequency of overall homozygosity for the DRB3/4/5 loci was observed in female patients compared to gender matched controls (RR = 2.8) and male patients. The previously demonstrated association of DQB1 homozygosity with CLL in general was found to be specific for female patients (RR = 4.4). Considering the lack of an a priori hypothesis which made it virtually impossible to obtain statistical significance it was not unexpected that none of the observed differences remained significant after correction for multiple comparisons. However, these results suggest a recessive, gender-specific susceptibility factor for CLL within or in vicinity of the human MHC class II region and should serve as an a priori hypothesis for future studies focusing on these gene loci. Furthermore, an increased frequency for HLA-Cw*06 was seen in patients with an early onset age (RR = 2.7) but lost significance after correction for multiple comparisons. The previously reported association of HLA-DRB4*0103 with CLL in general was observed in all groups irrespective of gender and age. Conclusively, our study supports the concept, that CLL represents a disease with a complex etiology and genetic susceptibility which appears to be influenced by the human MHC.