There is scarce data on the burden of leptospirosis and its epidemiological characteristics in Argentina. This study aimed to evaluate distribution of leptospirosis cases and identify risk factors for the disease during national laboratory-based surveillance. From January 1999 to December 2005, 812 suspected cases were referred to the national reference laboratory, of which 182 and 463 had respectively, laboratory confirmed and unconfirmed diagnosis of leptospirosis. The diagnosis of leptospirosis was discarded in 167 cases. The most prevalent presumptive infecting serogroup was Icterohaemorrhagie followed by Pomona, Ballum and Canicola. The majority of cases occurred during the worm and rainy months. Confirmed cases were predominantly adults and males, who presented with fever, headache and myalgias. Severe clinical manifestations included jaundice and acute renal insufficiency. Conjunctival suffusion, a hallmark clinical sign of leptospirosis, was found in 55% of confirmed cases, and 43% of the cases with discarded diagnosis (p=0.036). After multivariate analyses, age >30 years (OR=2.16; 1.05-4.41), occupation in a rural setting (OR=3.41; 1.45-8.06), contact with contaminated surface water (OR=2.17; 1.01-4.68), and contact with floods (OR=4.49; 1.17-17.25) were significantly associated with leptospirosis. In conclusion, although activities associated with rural occupations remain important risk factors in Argentina, exposures occurring during flooding events have emerged to be the major risk factor for leptospirosis.