Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease translating the different genetic and environmental factors involved. Polymorphisms at several loci, including the major histocompatibility complex (MHC), have been associated worldwide with SLE, although inconsistencies exist among these studies mainly due to genetic heterogeneity between populations and sample characteristics. The aim of the present study was to investigate in Portuguese SLE the association of HLA-DRB1 alleles with clinical patterns of the disease and severity. Two hundred eighteen Portuguese patients with SLE--42% of whom had kidney involvement--were studied for HLA-DRB1. Clinical and laboratory manifestations were correlated with HLA allele frequencies. HLA-DRB1 * 03 allele frequency was significantly higher in SLE patients--as a whole and as either with or without renal involvement--compared to controls, while HLA-DRB1 * 09 and DRB1 * 13 allele frequencies were decreased. Regarding the relationship with the presence or absence of specific clinical manifestations, it was only found that HLA-DRB1 * 08 allele frequency was increased in patients with neurological involvement. No association with the presence or absence of anti-dsDNA, anti-sm or antiphospholipid antibodies, or antiphospholipid syndrome, was observed. These results were reproducible when analysis was repeated only with patients with more than 5 years of evolution. As in other populations HLA-DRB1 * 03 is a susceptibility allele in Portuguese SLE patients, while HLA-DRB1 * 09 and DRB1 * 13 alleles may be protective alleles, not only for the disease, but for the development of nephritis. No correlations with the different clinical manifestations were found, except with the neurological system.