Self renewal of cancer stem cells, intrinsic and/or acquired drug resistance are the main factors preventing the anti- cancer therapy strategies for breast cancer. There are progressing studies to develop new therapeutic agents and to investigate the biomarker molecules to be targeted. In this study, a cDNA microarray analysis was performed in anticancer drug-paclitaxel resistant breast cancer cell line, which expresses the properties of breast cancer stem cells (BCSC). The drug sensitive parental MCF-7 cell line was used as control group. The genes overexpressed in BCSC-like cells that encode solute carrier (SLC) proteins were analyzed. According to the results, 21 SLC protein encoding genes were upregulated in the range of 2.0 and 35 folds. The genes, SLC38A5, SLC43A3, SLC6A15, SLC1A1, SLC2A3, SLC26A2, SLC22A15 and SLC16A3 are overexpressed about 9-35 folds. So, the related proteins may be regarded as potential targets and this will open a new research venue for the discovery of biomarkers to target breast cancer stem cells.