Polymerase chain reaction assay (PCR) amplifying a fragment of the Leptospira rrs gene was compared with culture and microagglutination test (MAT) for the diagnosis of leptospirosis in a study of 200 patients with various clinical syndromes compatible with leptospirosis. For the first group of samples tested, PCR identified the 14 cases that later were unequivocally confirmed to be leptospirosis. Thirteen other systemic cases presenting decreasing leptospiral antibody titers were also detected by PCR. The average persistence of leptospiral DNA in serum was estimated at 12 days, with a maximum of 56 days in a culture-confirmed case. The possibility of detecting leptospires in aqueous humor during the ocular complications of the disease was confirmed. The results suggest that PCR is an efficient tool for early diagnosis of leptospirosis during the first 10 days of the disease, especially when the clinical expression of the disease is confusing.