Recently, adverse effects of Polygoni Multiflori Radix(PMR) and Polygoni Multiflori Radix Praeparata(PMRP) have attracted intensive attention worldwide. These adverse effects most occurred in cases with high dose of prolonged medication course. Liver is usually the target organ of these adverse effects. In the present research, we performed in vivo chronic toxicity study and aimed to evaluate relationships between major constituents of water extractions and total anthraquinone of PMR and PMRP and chronic toxicity. SD rats of both sexes were given water extractions as well as total anthraquinone of PMR and PMRP for 12 weeks. We evaluated basic biochemical indexes, conducted microscopic observations of main organs and assessed early indicators of liver and renal fibrosis. Simvastatin, with hypertriglyceridemia and hypercholesterolemia as its main therapeutic areas, was investigated in our study. Component-toxicity relationships were also discussed. Five male rats died in our study, while all female rats survived, suggesting that some gender differences might be involved. Body weight was significantly changed, and basic biochemical indexes were sporadically occurred during the research. Pathological examinations on liver and kidney showed slight alternations after 12 weeks without dose-dependent relationship. Increase in serum laminin(LN) was observed in almost all male rats, indicating that the risks of liver or kidney fibrosis still existed, especially for males, although no fibrosis was found in the pathological examination of liver and kidney. No major and severe adverse effects were observed after 12 weeks of administration of PMR and PMRP. Regular safety monitoring is still necessary during medication in order to prevent possible risks.