Diagnosis of malaria based on the symptomatic approach has been associated with overtreatment. We sought to assess the magnitude of antimalarial drug use in pregnancy in order to contribute to the debate of introducing effective diagnostic tools for malaria. Methods: Data on malaria morbidity and treatment seeking practices were collected from pregnant women as part of a community intervention study testing new approaches to deliver intermittent preventive treatment of malaria in pregnancy in Mukono district, central Uganda. Results: A high proportion of pregnant women, 261/667 (39.1%) at the health units reported having fever; and of these 124/559 (22.2%) had positive smears for Plasmodium faciliparum. The symptom-based approach had a low sensitivity of 26.4%, leading to many pregnant women with malaria undiagnosed. Similarly, a high proportion of pregnant women, 145/383 (37.9%) with negative blood smears for P. falciparum received antimalarial drugs in addition to intermittent preventive treatment (IPTp) with sulfadoxine-pyrimethamine (SP). Conclusion: The results call for urgent strategies to identify effective diagnostic tools for malaria in pregnancy and to assess the negative effects of the over-use of antimalarial drugs in pregnancy.