Background: Plants are an important origin of natural substances that the raw material for various pharmaceutical and therapeutic applications due to the presence of phytochemicals, such as alkaloids. Alkaloids, which are found in different plant species, possess numerous biological activities. Some alkaloids have strong cytotoxic effects on various cancer cells. The search for new drugs to treat various cancers is one of the most important challenges of modern scientific research. Objective: This study aimed to investigate of cytotoxic activity of extracts that were obtained from Chelidonium Majus; Berberis sp.; Thalictrum foetidum containing various alkaloids on selected cancer cell lines. The aim was also the quantification of selected alkaloids in the investigated extracts by HPLC. Methods: The analysis of alkaloids contents were performed while using HPLC in reversed phase (RP) mode using Polar RP column and mobile phase containing acetonitrile, water, and ionic liquid. The cytotoxic effect of the tested plant extracts and respective alkaloids’ standards were examined while using human pharyngeal squamous carcinoma cells (FaDu), human tongue squamous carcinoma cells (SCC-25), human breast adenocarcinoma cell line (MCF-7), and human triple-negative breast adenocarcinoma cell line (MDA-MB-231). Conclusion: All of the investigated plant extracts possess cytotoxic activity against cancer cell lines: FaDu, SCC-25, MCF-7, and MDA-MB-231. The highest cytotoxic activity against FaDu and MDA-MB-231 cells was observed for Chelidonium majus root extract, while the highest cytotoxic activity against SCC-25 and MCF-7 cells was estimated for the Thalictrum foetidum root extract. There obtained significant differences in the cytotoxic activity of extracts that were obtained from the roots and herbs of Chelidonium majus and Thalictrum foetidum. Based on these results, investigated plant extracts can be recommended for further investigations of anticancer activity.