In present article was studied the separation process of pharmacological active total alkaloids from Chelidonium majus L. growing in Georgia. Alkaloids were extracted from medicinal herbal material and separated by liquid extraction, diluents gas and a microfiltration through membrane equipment. The obtained A1, A2, A3 fractions were analyzed by GC/MS method; in all cases separation proceeds by the principle of extraction of the target alkaloids. It was concluded that the A1 is enriched with α and β cryptopins, and protopin, but homochelidonine and chelidonine are in low contents. As accompanying alkaloid is identified dihydrosanguinarine as an artifact; the A2 is enriched with the maximum contents of stylopine and protopin, but the poor contents of chelidonine and homochelidonine; the A3 is enriched with α and β cryptopins and maximum content of chelidonine. Extraction of alkaloids from Chelidonium majus L. proceeds selectively, but depending on a way of separation of the total alkaloids allows varying qualitative and quantitative consistence of the final product.