BACKGROUND: No longitudinal data from population-based studies of eye disease in sub-Saharan-Africa are available. A population-based survey was undertaken in 2007/08 to estimate the prevalence and determinants of blindness and low vision in Nakuru district, Kenya. This survey formed the baseline to a six-year prospective cohort study to estimate the incidence and progression of eye disease in this population. METHODS/DESIGN: A nationally representative sample of persons aged 50 years and above were selected between January 2007 and November 2008 through probability proportionate to size sampling of clusters, with sampling of individuals within clusters through compact segment sampling. Selected participants underwent detailed ophthalmic examinations which included: visual acuity, autorefraction, visual fields, slit lamp assessment of the anterior and posterior segments, lens grading and fundus photography. In addition, anthropometric measures were taken and risk factors were assessed through structured interviews. Six years later (2013/2014) all subjects were invited for follow-up assessment, repeating the baseline examination methodology. DISCUSSION: The methodology will provide estimates of the progression of eye diseases and incidence of blindness, visual impairment, and eye diseases in an adult Kenyan population.