OBJECTIVE: To analyse the epidemiological profile of 488 cases of leptospirosis in Rio de Janeiro, Brazil between 1997 and 2002, using a variety of methods of spatial epidemiology, to establish alert guidelines in general hospitals, which might be a tool to improve diagnosis and treatment of leptospirosis to reduce lethality rates. METHODS: Scan statistics identified six space-time clusters, which comprised a range of 2 to 28 cases per cluster. Generalized linear mixed models were used to evaluate risk factors for a cluster case which incorporated individual characteristics and spatial information on environmental and climactic factors in a single model frame. RESULTS: Cluster case events were associated with heavy rainfall (OR 3.71; 95% CI 1.83-7.51). The model did not identify socioeconomic or environmental covariates that significantly influence the risk of developing a cluster rather than non-cluster case. CONCLUSION: Clustering of leptospirosis in this urban setting appears to be due to transmission during heavy rainfall.