OBJECTIVES The aim of this study was the first identification of Leptospira isolates from Azorean inpatients. METHODS Whole blood samples from 68 inpatients attending the São Miguel Hospital between 2006 and 2008, with a clinical and epidemiological suspicion of leptospirosis, were inoculated in a transport medium broth at the patient's bedside and further processed using a serial dilution technique prior to culture. At admission, 62 (91%) patients were also analyzed for the presence of leptospiral DNA by a nested PCR and 40 (59%) for specific agglutinins by microscopic agglutination test (MAT). The isolates obtained were first assigned at the serogroup level by both MAT reactivity with hyperimmune rabbit antisera and a PCR-based assay with the single primer iRep1. The species identification was performed by DNA sequencing. The use of monoclonal antibodies allowed intraspecific discrimination at the serovar level. RESULTS Of the 10 (14.7%) human Leptospira isolates, seven were identified as Leptospira interrogans serovar Copenhageni and three as Leptospira borgpetersenii serovar Arborea, which is in agreement with previous data from the Azorean rodent population. CONCLUSIONS This study represents a great step towards the definitive identification of the pathogenic leptospires in Azorean patients and confirms the bacteriological human-rodent connection for the first time.