The objective of this study was to use different methods to isolate and separate the bioactive compounds found in leaves and seeds of Datura metel and these methods include solvent extraction by chloroform and chromatography separation by sorbent material such as silica gel (Merck Column Extrelut^®1), as well as to study effect of deffating operation from seeds in separation of alkaloids. Results showed that weight percentage of alkaloids were 0.15, 0.36, 0.60 and 0.82% for seeds and leaves of Datura metel by solvent extraction and column chromatography respectively. High Performance Liquid Chromatographic (HPLC) was employed to analysis the extracts which proved that, the chromatography separation of alkaloids was more accurate and active than solvent extraction.