Ribosome-inactivating lectins (RILs) are A-B type toxins like ricin whose molecular target is the large rRNA of eukaryotic ribosome. Administration of lethal doses of the RIL nigrin b isolated from elderberry (Sambucus nigra L.) bark triggers specific intestinal derangement. The aim of the present research was to explore the early effects of a lethal dose of nigrin b (16 mg/kg body weight) on the small intestine using light and electron microscopy to ascertain intestinal epithelium changes. 6 h after nigrin administration, the small intestine crypts began to show signs of damage with cells appearing at different stages of apoptosis. 16 h after injection crypts appeared more impaired, including the derangement of Paneth cells. The novelty of our results is that the Paneth cells in the small intestine in addition to stem cells are the early cellular targets for nigrin b.