The prevalence of haemoparasites, leptospirosis and Yersinia pestis was investigated in rodents and shrews from Tanzania, Namibia and Swaziland. Blood smears originating from rodents and shrews from the three countries indicated the presence of Trypanosoma lewisi (72.7%; n =950), Bacillus spp. (25.6%; n =950), Borrelia sp. (0.01%; n =950) and bipolar coccobacilli (0.01%; n =950). The blood smears from Namibia (n =26) had no haemoparasites while only 1.33% (n =75) of those from Swaziland showed presence of T. lewisi. Leptospira interrogans was found in rodent blood sera from Tanzania in the following serogroup proportions (n =350): Icterohaemorrhagiae (10.29%), Pomona (2.86%), Hardjo (1.14%), Bullum (0.86%), Grippotyphosa (1.43%) and Canicola (1.14%). Serodiagnosis of antibodies against the F1 antigen of Y. pestis using the enzyme linked immunosorbent assay (ELISA) was negative for all the serum samples from central Tanzania, while two samples of serum from two species of rodents, Rhabdomys pumilio and Gerbilliscus leucogaster, collected in the Kavango Region of Namibia were positive. These results suggest an enzootic plague activity in this region in Namibia. It is concluded that zoonotic agents, that are infectious to humans, are prevalent in rodents and shrews in the three countries, and that local communities should apply rodent control measures to reduce the risk of human infections.