Most patients with chronic renal failure develop end-stage renal disease (ESRD) that requires renal transplantation. This study investigates the possible associations between human leucocyte antigen (HLA) Class I and Class II molecules with ESRD. Genotyping data (HLA) obtained between 2005 and 2009 on 235 unrelated Saudi patients (147 males, 88 females; mean age: 58 +/- 7 years) with ESRD awaiting renal transplantation were assessed retrospectively at the King Khalid University Hospital. Data were compared with the results on 60 normal, healthy, unrelated Saudi individuals (37 males and 23 females; mean age: 51 +/- 5 years). HLA Class I and Class II antigens were detected by lymphocytotoxicity and a polymerase chain reaction (PCR) method using DNA sequence-specific primers. Although present in small numbers, HLA Cw2 was found in significantly fewer patients (n = 11; 4.68%) compared to normal subjects (n = 9; 15%) and was found to confer protection against ESRD (P = 0.005; relative risk [RR]: 3.594, 95% confidence interval [CI]: 1.415-9.126). Among the HLA Class II antigens, HLA DQB1*03(8) was detected more frequently in the patient group (n = 65; 27.6%) than in the normal controls (n = 9; 15%) and was positively associated with risk of ESRD (P = 0.04; RR: 0.462, 95% CI: 0.215-0.991). No significant differences were observed between the two groups in respect of HLA-A2, HLA-B50(21), HLA-B51(5) and HLA-Cw7 (HLA Class I), and HLA-DRB1*04, HLA-DRB1*07 and HLA-DQB1*02 (HLA Class II). Occurrence of the most frequent HLA alleles was no different between the ESRD group and the controls. The protective role of HLA-Cw2 and the marginal susceptibility associated with HLA-DQBI*03(8) for ESRD requires further investigation.