Rodents are well-recognized reservoirs of Leptospira, contributing to its maintenance in endemic areas and playing a role in the public health risk associated with the infection. This study sought to provide some insights into rodent populations from Chile and their Leptospira carriage. In total, 393 rodents were trapped in 177 households. Higher rodent counts were associated with year 2 of the study, rainfall, and number of rodent signs. There was an inverse correlation with the number of cats. The number of rodents was higher in villages compared with slums (rate ratio = 3.23) but modified by average household age. Eighty rodents (20.4%) tested positive for Leptospira: 19.7% on the farms, 25.9% in villages, and 12.3% in the slums. Prevalence was 22.5% in Mus musculus, 20.7% in Rattus rattus, 21.1% in wild rodents, and 10.3% in R. norvegicus. Seasonal and temporal effects were the major determinants of Leptospira infection in rodent populations.