The main objective of this study was to evaluate the clinical differences and the pattern and extent of organ damage in late-onset systemic lupus erythematosus (SLE). A nested case-control study was performed from patients with SLE followed in the Rheumatology Unit of the State University of Campinas between 1974 and 2005. Patients who developed SLE after the age of 49 were considered late-onset SLE. SLE patients with age <49 years, matched for sex, ethnicity, disease duration and organ damage at study entry were randomly chosen to compose the control group. Baseline and cumulative clinical manifestations, laboratory data, SLE disease activity index (SLEDAI), Systemic Lupus International Collaborating Clinics/American College of Rheumatology-damage index (SDI) and mortality were compared between groups. At diagnosis and follow-up, late-onset group had lower SLEDAI scores when compared with younger age onset. Clinically, they presented less frequently arthritis (P = 0.0002) and malar rash (P = 0.02) and more frequently Raynaud's phenomenon (P = 0.002) and arterial hypertension (P = 0.02) when compared with young onset at diagnosis. Late-onset SLE received lower total corticosteroid dose (P < 0.001) and less frequently cyclophosphamide (P = 0.01). During the study period, late-onset SLE had always lower SLEDAI scores (P = 0.001). At study endpoint, late-onset SLE patients had significantly higher SDI scores (P = 0.001) and a higher mortality rate when compared with younger onset group (P < 0.01). In conclusion, late-onset SLE is milder on presentation and during course of disease, but patients have more organ damage and a higher rate of mortality than young onset SLE. Patients with late onset should be followed with close monitoring and early identification of complications is mandatory in this subgroup of patients with SLE.