There were about of 124 to 283 million cases of malaria with 367,000 to 755,000 deaths annually. This study aimed to assess the prevalence of malaria cases and associated risk factors among attendants at Chichu and Wonago health centers, South Ethiopia. In this health institution based cross sectional study, 324 subjects, attendants from outpatient department who came for any kind of medical services, were included during May to June 2016. A blood film examination format and structured questionnaire were used for data collection. Peripheral blood samples were collected and the presence of malaria cases was observed microscopically. The collected data were analyzed by SPSS version 20.0. Malaria cases were detected in 91 (28.1%) of the participants with higher infection rate amongst (56.04%). The predominant Plasmodium species detected was P. vivax (52.75%) followed by P. falciparum (35.16%) and mixed malaria infection by both of the species (12.09%). Housing construction and not using of insecticide treated bed nets for the last 6 months were significantly associated with the risk of getting malaria. Individuals who had stagnant water in their compound were more likely to get malaria than those who did not (OR=1.87, 95% CI: 1.20, 2.76). Houses that had been sprayed with insecticide in the past 6 months were protected against malaria infection (OR=0.33, 95% CI: 0.11, 0.92). Moreover, bed net utilization was associated with a significantly lower risk of infection (OR=0.19, 95% CI: 0.09, 0.37). Type of housing construction, not using bed net, insecticide spraying and residing near stagnant water were associated risk factors with malaria positivity in the study area.