Background: Malaria infestation in pregnancy is a major public health concern and ranks amongst the commonest complications of pregnancy in Nigeria. Approximately 50,000 Nigerian women die each year from largely preventable pregnancy related complications. Intermittent preventive therapy for malaria in pregnancy (IPTp) is a key recommendation in the National guideline for malaria treatment in Nigeria. This study assessed the prescription pattern of intermittent preventive therapy with Sulphadoxine-Pyrimethamine for pregnant women among doctors practicing in 68 Nigerian Army Reference Hospital, Yaba, Lagos, Nigeria. Methods: This was a retrospective study using case notes of pregnant women seen at antenatal clinic of 68 Nigerian Army Reference Hospital, Yaba, Lagos, Nigeria from January, 2008 to December, 2008. A total of 336 case notes were reviewed. The findings were precoded, data entry and analysis was done using EPI INFO 2002. Results: A good proportion of the women (82.9%) booked for antenatal clinic within the first and second trimesters of pregnancy. Most commonly prescribed by doctors was the weekly pyrimethamine (daraprim) for malaria prophylaxis in pregnancy (100.0%). Very few doctors prescribed intermittent preventive therapy with sulfadoxine-pyrimethamine, and the few who did prescribed just one dose. Conclusion: The study showed a very low level of prescription of IPTp among doctors practicing at 68 Nigerian Army Reference Hospital, Yaba, Lagos, Nigeria. There is a great need for training of these doctors and other health professionals on the recommendations of the current National Antimalarial Treatment Guidelines.