Tumorigenesis is a multi-step process involving several consecutive genetic alterations resulting in loss of genomic stability and deregulated signal transduction pathways. To study these deregulated processes in vitro, typically established cancer cell lines derived from primary tumors, ascites, or from metastases are used. However, these cancer cell lines reflect only late stages of the tumorigenic process. To better understand the consequences of the sequential genetic alterations in an in vitro model system, we applied consecutive immortalization and transformation of primary human mammary epithelial cells (HMECs) combining shRNA-mediated knockdown of tumor suppressor genes and overexpression of oncogenes. Thereby, we developed a panel of isogenic HMEC-derived cell lines reflecting the multi-step process of tumorigenesis. The immortalized cell lines have a normal epithelial morphology and proliferate indefinitely and anchorage-dependently. In contrast, the transformed cells exhibit mesenchymal-like morphological changes and strong colony-forming activity in soft agar. SNP array analysis showed that none of the cell lines displayed gross chromosomal aberrations in 80 % of the chromosomes. However, massive changes were observed in some chromosomes of the transformed cells indicating that the transformed phenotype is characterized by chromosomal alterations. The isogenic immortalized and transformed cells described here provide a powerful tool for the in vitro validation of target genes for cancer therapy.