Background: The overlap of symptoms, geographic and seasonal co-occurrence of Plasmodium, Leptospira and Rickettsia infections makes malaria diagnosis difficult, increasing the chances of misdiagnosis. The paucity of data on the prevalence Plasmodium, Leptospira and Rickettsia infections contributes to an overly diagnosis of malaria. We aimed to determine the prevalence and distribution of Plasmodium, Leptospira and Rickettsia infections in northern Tanzania. Methods: A community based, cross sectional survey was conducted in two sites in Northern Tanzania. PCR was used to detect Plasmodium, Leptospira and Rickettsia infections. Results: The prevalence of P. falciparum and Leptospira spp were 31/128 (24.2%) and 3/128 (2.3%), respectively. No Rickettsia infection was detected in any of the two sites. Taking study sites separately, Plasmodium infection was detected in 31/63(49.2%) of participants in Bondo while Leptospira infection was detected in 3/65(4.6%) of participants in Magugu. Plasmodium was not detected in Magugu while no Leptospira infections were detected in Bondo. Fever was significantly associated with Plasmodium infection (χ2= 12.44, p<0.001) and age (χ2=17.44, p=0.000). Conclusion: Results from this study indicate Plasmodium infection as the main cause of fever in the studied sites. While Plasmodium and Leptospira contribute to fevers, Rickettsia infection is an insignificant cause of fever in Northern Tanzania. Keywords: Neglected Infectious Diseases; Plasmodium; Leptospira; Rickettsia; co-occurrence; Tanzania.