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Background and purpose: In this study, we aimed to evaluate the anticancer activity of Physalis alkekengi extract encapsulated into chitosan nanoparticles on HT29 cell line. Materials and methods: The fruits of the P.alkekengi were collected from Kohgiluyeh Boyerahmad province in south-west of Iran and dried in a dark environment. Then, the hydroalcoholic extract of the plant was extracted by percolation and encapsulated into chitosan nanoparticles. The toxicity effect of three samples; chitosan alone, chitosan containing the extract and the extract of P.alkekengi was investigated using MTT assay. Finally, Annxin V/propidium iodide (PI) kit was used to study the apoptotic effect of samples. Results: According to the MTT assay, during 72 hours, the cytotoxicity effect of chitosan nanoparticles of 160 nm containing the extract increased significantly (P< 0.05). Moreover, the apoptosis assay indicated that chitosan nanoparticles containing the extract had more apoptotic effects than the extract alone (71% vs. 43%). Conclusion: P.alkekengi extract encapsulated into chitosan nanoparticles had more anticancer activity compared with that of the extract alone.