Patients with systemic lupus erythematosus (SLE) have a longer life expectancy. The occurrence of irreversible damage has become a major concern. The present study assessed damage progression in patients with SLE over a 2-year period and identified baseline features associated with damage accrual. Two hundred and twenty-one patients that fulfilled criteria for SLE and had a follow-up longer than 6 months were enrolled. Demographic, clinical, and immunological data were collected at baseline. Accumulated organ damage was scored using the Systemic Lupus International Collaborating Clinics/American College of Rheumatology damage index (SDI). Patients were prospectively followed and SDI assessment repeated at 2 years. At baseline 72 patients (33%) presented some irreversible damage, and after 2 years 53 had accrued new damage. The mean SDI for the whole cohort increased from 0.582 to 0.980. Damage progression was higher in ocular, cardiovascular, and musculoskeletal systems. Older age [OR = 1.045; 95% confidence interval (CI) 1.021-1.069; P = 0.03], presence of antiphospholipid antibodies (OR = 3.047; 95% CI 1.169-7.941; P = 0.02), steroid use (OR = 6.401; 95% CI 1.601-25.210; P = 0.008), azathioprine use (OR 3.501; CI 1.224-10.012; P = 0.01), and hypertension (OR = 3.825; 95% CI 1.490-9.820; P = 0.005) were predictors of damage progression in multivariate analysis. Overall SDI increased over time, with some systems being affected more frequently. Demographic and clinical characteristics, co-morbidity, and treatment options may contribute to irreversible damage. It is necessary to determine whether the control of modifiable factors (e.g., hypertension and judicious use of medications) might prevent damage progression in SLE patients.