Background: Leptospirosis is a zoonotic disease, transmitted by domestic animals and rodents. Rats are one of the rodent carriers of Leptospira bacteria. Rats are arboreal animals. Rats often found around the settlements, as Bandicota bengalensis, Rattus norvegicus and Mus muscullus. Some rat-borne diseases such as: plague, scrub typhus and leptospirosis. The aim of this study was to determine prevalence and the types of rats as the carrying Leptospira in Yogyakarta city. Methods: This study is an observational method with cross sectional design. The research included trapping and identification of house ratas, examination of Leptospira in rats. A total of 200 traps installed in all districts of Yogyakarta city, which leptospirosis cases reported between 2011-2013. The blood and kidneys rats were taken for leptospirosis examination by Polymerase Chain Reaction. Results: The research indicated that rats were captured amounted to 172, consisting outdoors were 18% and 82% indoors. There are three species rats that had been identified, i.e. Rattus tanezumi 82%, Suncus murinus 3.5% and R.norvegicus 14.5%. The prevalence of leptospirosis in rats were 12.7%.