Background: Yogyakarta is one of the largest cities in Indonesia. The city is crossed by three major rivers, which often cause flooding in some areas. Flooding is often hurt to all aspects of human life, including the post-flood disease. Environmental changes due to flooding will result in the spread of leptospirosis. Leptospirosis is one of rodent borne disease, which transmitted by leptospira infected in animal urine. The aim of the study was to determine the relationship of individual behavior on the incidence of leptospirosis in the Yogyakarta city. Methods: This study used a case control design. The data in this study is derived from the secondary data obtained from medical records of general hospital Yogyakarta city and through structured interviews using questionnaires that have been developed. Subjects were 130 people, where 65 positive leptospirosis as cases and 65 negative leptospirosis respondent as a control, with a ratio of 1: 1. Results: The results showed that behavior factors influencing the incidence of leptospirosis is the type of work (Odd Ratio (OR) = 2.6; 95% Confidence Interval (CI): 1.211 to 5.691; p value = 0.022) and a history of injury (OR = 4.2; 95% CI: 1, 93 to 9.14; p = 0.027). While the behavior is not a risk factor for leptospirosis cases are: contact with the carcass, using footwear, using soap, bathing in the river, hand washing, use of personal protective equipment, cover food and throw away leftovers. Conclusion: The type of work and history of injury as risk factors for leptospirosis cases in Yogyakarta city.