Background: Epilepsy is one of the major brain disorders worldwide. Breakthrough seizures carry a heavy burdenof epilepsy, with increased morbidity and risk of premature mortality. Several factors have been suggested toprecipitate break through seizures but these have not been studied in our setting. The study sought to determinethe prevalence of breakthrough seizures, as well as precipitating factors in adults with epilepsy attending Mulagohospital.Methods: This study was conducted in Mulago Hospital, using a cross sectional study design between August andDecember 2009. Subjects with epilepsy and had been receiving anti-epileptics treatment for at least 6 months priorto the study were consecutively enrolled.Results: A total of 256 patients with epilepsy were recruited. Prevalence of breakthrough seizures among epilepsypatients attending Mulago hospital was 75.3%. Factors found to be significantly associated with breakthroughseizures were non compliance to anti-epileptic therapy (p < 0.0001); duration of treatment (p < 0.0001); infections (p< 0.044) and menses among female study participants (p < 0.0001). The level of education, sleep deprivation, alcoholand substance abuse, and flickering lights were not associated with breakthrough seizures.Conclusions: Breakthrough seizures are high in Mulago National referral hospital, with drug non-compliance thecommonest cause. The attending physicians need to identify precipitating factors among patients attendingMulago hospital and have them addressed appropriately during patient care.