The study aim to determine the chemical compounds in aqueous and methanolic extracts of Datura innoxia seeds and leaves and to evaluate their toxic effects on experimental rats. Seeds and leaves were collected from El-Obied, North Kordofan State, Sudan, in October, 2016. The aqueous and methanol extracts were carried out by using maceration method and soxhlet apparatus respectively. Sixty five male Albino Wistar rats, three months old and with an average body weight ranged 110-120 g, were randomly divided into thirteen Groups, consisting of five rats in each Group. Group 1 served as control and fed with normal rats’ food and water for thirty days. Groups 2, 6 and 10 administered aqueous seeds extract, Groups 4, 8 and 12 received methanol seeds extract, Groups 3, 7 and 11 received aqueous leaves extracts, Groups 5, 9 and 13 received methanol leaves extract, all the Groups received the same type of extract were administered 40, 60 and 80 mg/kg body weight respectively. The extracts administered to the rats intra gastrically using cathodal tube daily for thirty days. The effects of oral administration of leaves and seeds extracts to 60 healthy rats over 30 days were evaluated by histological studies and body weight changes. The analysis by gas chromatography-mass spectrometry (GC-MS) of aqueous and methanolic extracts revealed the presence of alkaloids (Scopolamine, atropine and Hyoscyamine), fatty acids, esters, amides, amino acids, ketones, coummarins, terpinoids, phenols, alcohols and hydrocarbons compounds. The histological results showed that administration of extracts caused pathologic changes in the organs studied. The treated Groups had lower (p ≤ 0.05) body weight gains than control Group. The study concluded that the toxicity of seeds and leaves (methanolic and aqueous) extracts are nearly have the same toxic effects on rats due to their same active ingredients (alkaloids) and the oral administration of the extracts was found to be safe up to 40 mg/kg.