The purpose of the present study was in vitro determination of the combined effects of doxorubucin and 5-fluorouracil by 2D and 3D culture conditions on breast cancer using MCF-7 cell line and CSCs isolated from these cells. In the first stage of this study, CSC isolation and their characterization were performed. In the next experimental period, the antiproliferative effects of 5-Fu and Dox on the MCF-7 and CSCs were demonstrated on 2D. To evaluate the synergistic/antagonistic effects of these chemotherapeutics, the CI was calculated. Additionally, 3D tumor spheroids were used as another model. In the last step, qRT-PCR analysis was performed to examine apoptosis-related gene expressions. In this study, it was clearly seen that CSCs obtained from the breast cancer cell line express stemness factors. In addition, the antiproliferative effects of 5-Fu and Dox on breast cancer and associated CSCs were very clear. Their synergistic effects were determined by CI values. Moreover, it was seen that combined theraphy changed the expression levels of genes related to apoptosis. Additionally, it was molecularly demonstrated that 3D tumoroids were more resistant than the others. In conclusion, the polychemotherapeutic approach was much more effective than the monotherapy. The fact that this effect was seen not only in breast cancer cells, but also in breast cancer stem cells. In addition, it was very promising that the results obtained were similar in both two-dimensional and three-dimensional tumoroids.© 2024. The Author(s).