Twenty‐three cases of microvillous atrophy were reviewed to determine clinical and morphological characteristics of the disease. Congenital and late‐onset forms of presentation were clearly identified in which the late‐onset cases appeared to have a better prognosis. Three different, and distinctive, appearances of the proximal small intestinal mucosa were found. Careful orientation of mucosal samples allowed a temporal sequence of events to be delineated in which the first morphological abnormality to be detected in the epithelium was the accumulation of “secretory granules”; microvillous inclusions were seen in older cells in the upper villous region. It is suggested that, in familial microvillous atrophy, diarrhoea and disorganisation of the brush border assembly occur as a consequence of a more fundamental defect that affects the intracellular traffic of certain cell components, as indicated by the accumulation of “secretory granules.”