Rats was the group rodent who made disorder on various human life in agricultural, economy and healthy. Rats was a carrier for some pathogenic microbes caused infectious disease. Most rodents are animals commensal including Norway (Rattus norvegicus), house rats (Rattus rattus) and wirok (Bandicota bengalensis). Leptospira usually attacks rats, both the ditch rats and house rat. This study was conducted to know the spread pattern rats infected Leptospira in Yogyakarta. This study is an observational method with cross sectional design. The research included trapping, identification, and examination of Leptospira in rats. A total of 200 traps installed in all districts of Yogyakarta city, which leptospirosis cases reported from 2011 to 2013. The blood and kidneys rats were taken for leptospirosis examination by Polymerase Chain Reaction. The geographical positions of rats was located using the GPS. The spread pattern and spatial autocorrelation was analyzed by spatial autocorrelation Moran index and Average Nearest Neighbor. The result showed that Moran index: -0.4151, Z score: -0.3199 with Z -α/2:-2.58. By Average Nearest Neighbor (ANN) analysis, Z score: 9.569, with ANN: 3.237 >1. It can be concluded that there was a spatial relation the spread of rats infected Leptospira and the spread pattern was dispersed.