Microscopic (light and electron) and histochemical abnormalities have been demonstrated in the jejunum of rats with the blind loop syndrome. Three groups of animals were studied: normal control animals, and animals with either self-filling (SF) or self-emptying (SE) blind loops. Vitamin B12 malabsorption and bacterial overgrowth occurred only in those animals with SF blind loops. Three jejunal segments were studied: the blind loop segment and the jejunal segments proximal and distal to the blind loop. In the animals with the blind loop syndrome, those with SF blind loops, the most striking findings occurred in the blind loop itself, with similar but less marked changes in the jejunum distal but not proximal to the blind loop segment. Hypertrophy of both crypts and villi was evident with focal abnormalities of villus architecture. Approximately 10 to 20% of the columnar cells in the upper half of the villi were swollen and vesiculated. By electron microscopy microvilli demonstrated a variety of degeneration changes and the glycocalyx and terminal web were disrupted. Mitochondria and endoplasmic reticulum (ER), both smooth and rough, were swollen. Concentric whorls of parallel membranes and long, curvilinear rough ER were present in the cytoplasm. Histochemically, there was loss of enzymatic activity in the epithelial brush border, mitochondria and ER. Inasmuch as bacterial invasion of the jejunal mucosa was not seen, the etiology of these changes is not known but may involve bacterial "toxins" or products of bacterial metabolism. These morphological observations demonstrate that both brush border and intracellular injury occur in the jejunal epithelial cell of rats with the experimental blind loop syndrome.