OBJECTIVES: To determine how diagnosis of malaria may be improved by combining the use of rapid diagnostic tests (RDTs) for Plasmodium falciparum malaria with clinical diagnosis by the presence or history of fever compared with clinical diagnosis alone in emergency situations with flood-affected displaced populations in Mozambique. STUDY DESIGN: A cross-sectional study conducted at the emergency outpatient clinic in a village in the Chòkwè district of Gaza Province, 3 weeks after Cyclone Eline hit Mozambique in February 2000. METHODS: A hundred and thirty children aged less than 15 years with clinical malaria were selected for examination by RDT and fluorescent microscopy using acridine orange as a reference test. The diagnosis of clinical malaria was made by a history of fever in the last three days or axillary temperature above 37.0 degrees C at the time of attending the emergency outpatient clinic. Two positive predictive values were calculated; RDTs combined with clinical diagnosis and clinical diagnosis alone. RESULTS: Positive predictive values of RDTs combined with clinical diagnosis by the presence of fever or history of fever were 87.6% (92/105) (95% confidence interval (CI) 80.8-92.8) compared with 74.6% (97/130) (95% CI 66.2-81.8) for clinical diagnosis alone. Five patients were diagnosed false negative. CONCLUSION: RDTs combined with clinical diagnosis has sufficient positive predictive value to be used in emergency situations, while RDTs could result in increasing failure to treat when they are used for decisions of treatment compared with clinical diagnosis alone.