All studies attempting to find an association between vitamin D deficiency and cerebrovascular diseases have been conducted at latitudes far away from the Equator, where living conditions, cardiovascular risk factors, and sunshine exposure are different from tropical regions. We aimed to assess cerebrovascular correlates of vitamin D deficiency in community-dwelling older adults living in Atahualpa, a village located in rural coastal Ecuador. Out of 267 individuals enrolled in the neuroimaging substudy of the Atahualpa Project, 220 (82%) signed the informed consent. Mean age of participants was 70·9 ± 7·8 years, and 126 (57%) were women. Fifty-four (25%) persons have vitamin D levels <20 ng/ml, 47 (21%) had ischemic strokes, and 53 (24%) had moderate-to-severe white matter hyperintensities of presumed vascular origin. Exposure effect models constructed with vitamin D deficiency as the exposure, white matter hyperintensities and ischemic stroke as the outcomes, and confounders – age, gender, body mass index, physical activity, blood pressure, fasting glucose, total cholesterol, ionized calcium, phosphorus, intact parathormone, and serum creatinine – as independent variables revealed a significant association of vitamin D deficiency with white matter hyperintensities (P = 0·006) but not with ischemic strokes (P = 0·359). This study shows an association of vitamin D deficiency with diffuse subcortical brain damage in older adults living in a tropical region. Lack of awareness of the importance of vitamin D deficiency might be one of the factors influencing the high prevalence of white matter hyperintensities of presumed vascular origin in underserved Latin American populations.