To further evaluate the nature of the HLA association with alopecia areata (AA), we investigated the HLA-DRB1 locus in 161 AA patients and 165 matched controls from Belgium and Germany. HLA-DRB1 typing was performed using a recently established method that employs a combination of PCR-SSP (sequence specific priming) and Pyrosequencing(TM) technology. No significant differences were observed for HLA allele groups DRB1 *01, *07, *08, *09, *10, *11, *13, *14, *15, and *16. HLA-DRB1*03 was found to confer a protective effect (7.5% versus 13.6%, p = 0.011). Additional genotyping at the allelic level revealed a significant difference in HLA-DRB1*0301 between patients and controls (6.8% versus 11.2%, p = 0.048). The DRB1*04 allele group was confirmed as a risk factor for the development of AA (20.8% versus 13.3%, p = 0.012), with the allele DRB1*0401 accounting for the greatest proportion of the effect (13.4% versus 7.3%, p = 0.014). Results obtained after subgrouping of the patients according to age at onset, severity and family history of the disease suggests that the genetic effects of the HLA system are strongest in familial cases of the disease.