BACKGROUND Neuroimaging features associated with vascular cognitive impairment have not been examined in sub-Saharan Africans. We determined magnetic resonance imaging (MRI) features associated with cognitive impairment in a sample of Nigerian stroke survivors. METHODS Stroke survivors underwent brain MRI with standardized assessment of brain volumes and visual rating of medial temporal lobe atrophy (MTA), and white matter hyperintensities (WMH) at 3 months post-stroke. Demographic, clinical and psychometric assessments of global cognitive function, executive function, mental speed and memory were related to changes in structural MRI. RESULTS In our pilot sample of 58 stroke survivors (60.1 ± 10.7 years old) MTA correlated significantly with age (r = 0.525), WMH (r = 0.461), memory (r = -0.702), executive function (r = -0.369) and general cognitive performance (r = -0.378). On univariate analysis, age >60 years (p = 0.016), low educational attainment (p < 0.001 to p < 0.003), total brain volume (p < 0.024 and p < 0.025) and MTA (p < 0.003 to p < 0.007) but not total WMH (p < 0.073, p = 0.610) were associated with cognitive outcome. In a two-step multivariate regression analysis, MTA (p < 0.035 and p < 0.016) and low educational attainment (p < 0.012 and p < 0.019) were sustained as independent statistical predictors of cognitive outcome. CONCLUSIONS Medial temporal lobe atrophy was a significant neuroimaging predictor of early post-stroke cognitive dysfunction in the Nigerian African stroke survivors. These observations have implications for a vascular basis of MTA in older stroke survivors among sub-Saharan Africans.