Simple SummaryLeptospirosis is a zoonosis caused by pathogenic Leptospira, and synanthropic and wildlife species of rodents are an important source of infection; however, much of the information about the progression of the infection was obtained from lab murine models. The aim of this study was to assess infection status and risk factors by pathogenic Leptospira in synanthropic and wild rodent species and describe histopathological lesions in several organs from naturally infected animals. In this study, 121 rodents from three synanthropic species and two wild species were trapped within dairy farms in Southern Chile, where the bacteria were present. Liver, heart, kidney, and lungs from trapped animals were analyzed by different techniques to detect if the lesions present were produced by the bacteria. A large proportion of animals were identified as infected that were not detected by the microscopic agglutination test. There is a lower risk of infection in the fall compared to the rest of the seasons, and the synanthropic species has a lower risk of infection in comparison with wildlife species. Immunohistochemistry and quantitative real-time lipL32 polymerase chain reaction contributed to identifying the presence of pathogenic Leptospira in related histological lesions and 50% more infections than serology.Leptospirosis is caused by pathogenic Leptospira, and synanthropic and wildlife species of rodents are an important source of infection; however, much of the information about infection progression was obtained from murine models. The aim of this study was to assess infection status and risk factors associated with pathogenic Leptospira in synanthropic and wild rodent species and describe histopathological lesions in several organs from naturally infected animals. In a cross-sectional study, 121 rodents from three synanthropic species and two wild species were trapped in dairy farms in Southern Chile. Liver, heart, kidney, and lungs from trapped animals were fixed in formalin and stained with hematoxylin–eosin. Tissues with lesions consistent with Leptospira infection were tested by immunohistochemistry (IHC) and real-time polymerase chain reaction (qPCR) using the LipL32 antigen. Risk factors were assessed by a conditional mixed-logistic regression model. More than half (56.7%) of the negative reactors to the microscopic agglutination test were identified as infected either by IHC/qPCR. A lower risk of infection compared to the rest of the seasons was found in the fall, and the synanthropic species have a lower risk of infection in comparison with the wildlife species. IHC and qPCR contributed to the identification of pathogenic Leptospira in related histological lesions and 50% more infections than serology.