BACKGROUND: Asymptomatic malaria infection in refugees is both a threat to the lives of the individuals and the public in the host country. Although South Africa has been experiencing an unprecedented influx of refugees since 1994, data on malaria infection among refugees is lacking. Such information is critical since South Africa is among the countries that have planned to eliminate malaria. The objective of this study was to determine prevalence of asymptomatic malaria infection among a refugee population living in a city of KwaZulu-Natal province, South Africa. METHODS AND FINDINGS: A survey was conducted on adult refugee participants who attended a faith-based facility offering social services in a city of KwaZulu-Natal province, South Africa. The participants were screened for the presence of malaria using rapid diagnostic tests and microscopy. Demographic data for the participants were obtained using a closed ended questionnaire. Data was obtained for 303 participants consisting of 51.5% females and 47.5% males, ranging from 19 to 64 years old. More than 95% of them originated from sub-Saharan African countries. Two hundred and ninety participants provided a blood sample for screening of malaria. Of these, 3.8% tested positive for rapid diagnostic test and 5.9% for microscopy. The majority of malaria infections were due to Plasmodium falciparum. CONCLUSIONS: The study confirms the presence of asymptomatic malaria infections among a refugee population residing in a city of KwaZulu-Natal province that is not endemic for malaria. The results have important implications for both public health and malaria control in South Africa, particularly since the country has decided to eliminate malaria by 2018. To achieve this goal, South Africa needs to expand research, surveillance and elimination activities to include non-endemic areas, particularly with high refugee populations. We further recommend use of powerful diagnostic tests such as PCR for these interventions.