Berberis vulgaris and berberine, its main component, traditionally have been used for treatment of various disorders. The pharmacological properties of them have been investigated using different in vivo and in vitro models. In spite of beneficial effects of B. vulgaris on different cell lines, there are documents have revealed negative impacts of it on animal and human. In this regards, the determination of its toxicity in a scientific view is necessary. In current report, we provide classified information about the toxicity of B. vulgaris and berberine in different conditions consist of acute, sub-acute, sub-chronic and chronic state. Besides, it discusses the cytotoxicity, genotoxicity, mutagenicity, and carcinogenicity of B. vulgaris and berberine as well as developmental toxicity and clinical studies. Data from the present study indicate that their toxicity is depending on the route and duration of administration. According to present study, they could induce GI upset and ulceration, immunotoxicity, phototoxicity, neurotoxicity, cardiotoxicity and jaundice in a dose dependent manner. They should be used with caution in pregnancy, neonatal and G6PD deficiency. Besides, consideration should be taken in co-administration of berberine with drugs that are metabolized with CYP enzymes due their inhibitory effects on these enzymes. Furthermore, they evoke cytotoxicity on both normal and cancer cell line which is time and concentration dependent.