The use of plants as a source of medicine is an important component of the health care system in rural India. Carex baccans (Cyperaceae) and Potentilla fulgens (Rosaceae) have been known since ancient times in northeast India for their antitumor, antidiabetic, and antihelmintic properties. The present study was designed to determine the subacute toxicity profile of the root tuber extract of C. baccans and root-peel extract of P. fulgens in Wistar rats. The subacute oral toxicity was conducted using sublethal doses of 40, 50, 100, 150, 200, and 400 mgkg−1 body weights. Surface topographical and ultrastructural observations of liver and intestinal microvilli showed remarkable deformation and disruption, accompanied by quantitative changes in the liver enzymes, i.e., aspartate aminotransferase and alanine aminotransferase in comparison to those of the control group. Apoptotic cell death was observed in the liver cells of rats exposed to both of the plant extracts. A significant increase in splenic lymphocyte count was also observed in rats exposed to the highest concentration of both extracts. The results showed that consumption of the plant extracts at higher doses may cause toxicological effect if treatment continues for a long time.