|INTRODUCTION: Thyroid disorders have been associated with a number of pregnancy- related poor outcomes. Thyroid function assessment is not a common factor assessed for during a mother’s attendance of the antenatal clinic. The maternal and perinatal mortality rates in Uganda are still unacceptable and have remained stable over the past decade, thyroid disorders in particular hypothyroidism have been shown to affect perinatal mortality and morbidity. Other disorders are also responsible for several contributing factors to both maternal and perinatal mortality. The maternal mortality rate in Uganda is 506 per 100,000 live births and perinatal mortality is 43 per 1000 live births, (UDHS 2002). No studies have assessing for thyroid disorders in pregnancy have been done in Uganda as yet. Studies done worldwide point to a possibility of a significantly high number of people with those disorders in resource limited countries. And more so among women in the reproductive age group. These disorders, in particular hypothyroidism, are even more prevalent in areas with low dietary iodine. Studies done in Uganda assessing the total goiter rate, which is an indication for low iodine intake, have shown that iodine deficiency exists and should be declared a public health problem. OBJECTIVE: The study was aimed at determining the existence of thyroid deficiency in pregnancy in order to propose a screening programme for early diagnosis and prompt treatment. STUDY DESIGN: A Cross-sectional descriptive study. METHODS: From November 2006 to Febrauary 2007,200 mothers attending antenatal care in Lower Mulago hospital were recruited by systematic random sampling, interviewed to complete a demographic and sexual health questionnaire. Following informed conscent, eligible participants had a general obstetric examination, examination for an enlarged thyroid gland and had a blood sample was obtained and transported to the laboratory at -4Oc. Specimens were centrifuged and serum aliquots stored at -10oC . Batches of the samples were run with the IMX SYSTEM machine for thyroid function using the ultra sensitive Htsh Kit for TSH, Free T4 kit for T4 and Free t3 Kit for T3. DATA MANAGEMENT: Data was collected using a pre-tested interviewer administered questionnaire and analyzed using Epi-Info and SPSS software package. RESULTS: The prevalence of thyroid deficiency was 9.5%. No significant association with age, parity, marital status, alcohol intake and history of poor maternal and neonatal outcome was found. However, the study managed to demonstrate a protective effect to Hormonal contraceptive use on hypothyroidism with a risk about 8 times for non-users compared to users. CONCLUSIONS: The prevalence of thyroid deficiency in pregnancy among the 200 women studied was 9.5% in mulago hospital.. It might not be possible to identify a group of pregnant women at risk for thyroid deficiency based on age, parity, socio-economic factors and history of adverse outcomes without doing sensitive TSH screening. Ever use of hormonal contraceptives was protective against hypothyroidism. This study also demonstrated that hypothyroidism is still more prevalent than hyperthyroidism. Despite the fact that hypothyroidism was significantly prevalent, widespread screening during antenatal attendance could not be justified from this study.