Limbal epithelial stem cell deficiency (LSCD) occurs as a result of damage to the limbal epithelial stem cells (ESC) population. It may derive from direct destructive loss of the ESC (common chemical burn), and/or from dysfunction of the SC niche, leading to delayed death of the cells. This review focuses on delayed-onset LSCD, induced by antineoplastic chemicals, such as mitomycin C, 5-fluorouracil, and mustards, in terms of pathogenesis and management. These agents are used in ocular surface chemotherapy, in ocular surgery procedures, and as warfare agents, and target proliferating cells as slow-cycling cells, such as the ESC, are relatively resistant. Although the mechanism of the delayed loss of ESC is not entirely clear, we have shown, in the rabbit model, pathologic alterations in the limbal stroma, following the application of sulfur mustard, suggesting that dysfunction of the niche triggers the death of the SC later on. The absence of direct cytotoxic effects of these agents on the ESC, indicates a therapeutic window for prevention of the delayed LSCD.