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Leptospirosis is a neglected zoonotic disease that disproportionately affects poor populations in the world. Prevalence data in human populations in pastoral communities has been shown to be high. The disease is therefore contributing to an unknown toll on livestock productivity as well as human health in these areas. Rodent populations in irrigated areas of Kenya have also seen a rise and this could lead to an increase transmission of rodent-borne diseases. This pilot study therefore aimed at demonstrating the presence of the bacteria in rodent carriers in Tana River and Garissa counties of Kenya, areas that are characterized by irrigation and pastoral activities respectively. Kidney and blood samples from 67 rodents previously collected from these areas (mainly mice and multimammate rats) were analyzed using PCR. Prevalence of leptospires in rodent carriers was found to be 41.8% (28/67). Prevalence in the towns was: 16% (4/25) in Bura; 42% (8/19) in Hola; 82% (9/11) in Ijara and 58% (7/12) in Sangailu. Prevalence was found to be influenced with the area of sampling, with rodents from the pastoral areas being more likely to have the bacteria than those from the irrigated areas (Odds Ratio = 6.095). Prevalence showed no association with the species and age of rodents. Sequencing data revealed the species in circulation among rodents is Leptospira interrogans. This pilot study is one of the few to demonstrate the bacteria in rodent carriers in North-Eastern Kenya, which illustrates the underplayed public health importance of the disease in this part of Kenya. The high rodent prevalence of these bacteria poses risk of transmission of the …