Abstract Background Microalbuminuria is an early manifestation of kidney damage and independently predicts cardiovascular disease (CVD). Left ventricular hypertrophy (LVH) is also an early marker of cardiac manifestation of target organ damage among hypertensive patients. The prognostic significance of microalbuminuria and its correlation with left ventricular hypertrophy has not been extensively studied in African adult hypertensive populations. This study aimed at determining the prevalence of microalbuminuria, LVH in patients with microalbuminuria and the correlation between microalbuminuria and LVH among newly diagnosed black adult hypertensive patients attending a large outpatient hypertension clinic or admitted on the cardiology ward at Mulago national referral and teaching hospital and Uganda Heart Institute in Kampala, Uganda. Methods In this cross-sectional study, 256 newly diagnosed eligible black adult hypertensive patients attending the outpatient hypertension clinic or admitted on the cardiology ward at Mulago national referral and teaching hospital and the Uganda Heart Institute, Kampala Uganda were consecutively recruited over a period of 5 months. Data on socio-demographics, clinical and laboratory findings of the study participants was collected using a pre tested questionnaire. Two spot urine samples were collected to assess for microalbuminuria. Echocardiography (ECHO) was done to assess for the left ventricular mass index using the formula of Teicholz as evidence for early hypertensive heart disease. Results The mean age/standard deviation of the study participants was 54.3 ± 6.2 years with a female predominance (162, 63.3 %). The prevalence of microalbuminuria among newly diagnosed hypertensive patients was 39.5 %. The prevalence of LVH among patients with microalbuminuria was found to be 17 %. There was a positive correlation between microalbuminuria and left ventricular hypertrophy among the newly diagnosed adult hypertensive patients at Mulago Hospital (r = 0.185, p = 0.003). Conclusions This study demonstrates that microalbuminuria is highly prevalent among newly diagnosed black hypertensive patients and in the presence of LVH. There is also a positive correlation between microalbuminuria and LVH among newly diagnosed hypertensive patients. Since it is a less .