This study described the clinical features and complications of leptospirosis among patients seen at nine tertiary hospitals from September 28 to November 30, 2009 after a heavy rainfall typhoon. The clinical findings of the confirmed cases were compared with the previous clinical studies on seasonal leptospirosis in the Philippines. Risk factors for complicated disease were also identified. Confirmed cases were based on any of the following: positive leptospiral cultures of blood or urine, single high leptospira microscopic agglutination test (MAT) titer of 1:1,600, a fourfold rise in MAT, and/or seroconversion. Of 670 patients with possible leptospirosis, 591 were probable by the WHO criteria, 259 (44%) were confirmed. Diagnosis was confirmed by MAT 176 (68%), by culture 57 (22%), and by MAT and culture 26 (10%). The mean age of the confirmed cases was 38.9 years (SD 14.3). The majority were males (82%) and had a history of wading in floodwaters (98%). The majority of the patients presented with nonspecific signs, with fever as the most common (98.5%). Other findings were myalgia (78.1%), malaise (74.9%), conjunctival suffusion (59.3%), oliguria (56.6%), diarrhea (39%), and jaundice (38%). Most of the patients presented with a moderate-to-severe form of leptospirosis (83%). Complications identified were renal failure (82%), pulmonary hemorrhage (8%), meningitis (5%), and myocarditis (4%). Mortality rate was 5%, mostly due to pulmonary hemorrhage. This study emphasizes the importance of public awareness and high index of suspicion among clinicians of leptospirosis during the monsoon months when flooding is common. Early recognition and detection of the disease should decrease morbidity and mortality.