Until recently, little has been known about the morphological features of dying enterocytes at the villus tips of the human small intestine. The present study aimed to show the exfoliating processes of effete enterocytes at the villus tips. Cellular elements of the duodenal lumen and jejunal tissue in humans were fixed and processed for DNA nick end labeling (TUNEL), and transmission and scanning electron microscopy (TEM and SEM). Most cellular elements in the duodenal lumen were enterocytes having TUNEL-positive nuclei. By SEM, protruding enterocytes were discerned at the villus tips. Using the SEM samples embedded in epoxy resin, protruding enterocytes were observed at the villus tips by TEM; they were shrunk by forming numerous clear and autophagic vacuoles, took dome-like profiles, and possessed nuclei with chromatin condensation. The intercellular spaces beneath these protruding or effete enterocytes were often occupied by large lymphocytes. By TUNEL reaction, positive stainings appeared in the epithelium not only at the tip of the villi but also around the site. The results suggest that effete enterocytes at the villus tips of human small intertine are first shrunk by forming clear and autophagic vacuoles, and showed that their nuclei exhibit chromatin condensation immediately before being exfoliated into the lumen.