The effect of protein-energy malnutrition (PEM) on the structural development of rat jejunal absorptive epithelial cells was evaluated. Stereologic characteristics of jejunal histologic subcompartments, epithelial cell surfaces and volumes, and volumes of key subcellular organelles (nuclei, mitochondria, Golgi apparatus, lysosomes) in crypt and villus mid and tip cells were determined by morphometric analysis of light and electron micrographs in well-nourished rats and rats with PEM. In rats with PEM there were developmental alterations in cells migrating on villi that were not seen in crypt cells. The amplification of the apical microvillus surface between mid and tip levels in well-nourished rats (679-1085 micron2/cell) failed to occur in rats with PEM (807-729 micron2/cell). This resulted in an estimated 60% reduction of total jejunal absorptive surface, from 10,070 cm2 in well-nourished rats to 3975 cm2 in rats with PEM. In contrast, the development of the basolateral surface, which requires much less membrane accrual, was unaffected by PEM. Villus mid and tip cells of rats with PEM also had increased cell volume and mitochondrial volumes. Microvillus surface area per cell appears dependent on the number of microvilli per cell, which equals the cell flat surface times the microvillus numerical density (number of microvilli per square micrometer) in well-nourished rats. However, this relationship was not demonstrable in rats with PEM.