Background: Leptospirosis is a public health problem in the world, especially in tropical and subtropical countries with high rainfall. Transmission of leptospirosis can be occured directly with infected animals or indirectly through soil and water which have been contaminated by infected animal urine. Leptospira bacteria in the rodent is the most dangerous type compared with another bacteria in domestic animals. The aim: The aim of this study was to identify Leptospira bacteria serovar in rodents in Yogyakarta city. Methods: This study used cross sectional method. The population in this study were all of rodents that trapped in Yogyakarta region which reported in 2011-2014, included inclusion and exclusion criterias. Rodents were trapped by mousetrap (live trap) and then identified based on the characteristics of rodents. A total of 172 samples of rodents were collected, kidney and serum collection were conducted for examination. Positive or negative leptospirosis examination were conducted by PCR (Polymerase Chain Reaction) at Research and Development Center, Banjarnegara and Leptosira bacteria serovar examination was conducted by using MAT method (Microscopic Aglutinantion Test) at Veterinary Research Centre, Bogor. Results: The results showed that positive leptospirosis rodent (12,8%). (13.28%) of house rat (Rattus tanezumi) and (12.5%) of wirok rat (Bandicota bengalensis). From 9 samples of positive leptospirosis serum, all of samples showed negative reaction to 14 antigen collections of Leptospira bacteria at Veterinary Research Centre, Bogor. Conclusion: Leptospica bacteria serovars in rodent in Yogyakarta city with MAT examination are not from suspected serovars.