Single-cell transcriptome analysis provides information on the characteristics of individual cells in heterogeneous tumor tissues. We isolated more than 500 unsorted single cells from 11 breast cancer tissues for RNA-seq. Based on the copy number variation inferred from RNA-seq data, we could separate tumor cells with variable copy numbers over the genome from non-cancer cells without apparent changes in copy numbers. At a single cell level, carcinoma cells showed common features within each breast cancer subtype, and also intra-tumoral genetic heterogeneity with mixed signature of different breast cancer subtypes. Non-cancer cells consisted of immune cells with three distinct populations of T lymphocytes, B lymphocytes, and macrophages. T lymphocytes and macrophages displayed immunosuppressive characteristics; regulatory or an exhausted phenotype. Single cell trascriptome profile could figure out the range of intra-tumoral heterogeneity, and also immune cell profiles within breast cancer tissue, which might determine the response to immunotherapy.