In this model study, we developed a method to distinguish between breast cancer cells and normal epithelial cells, which is in principal suitable for online diagnosis by Raman spectroscopy. Two cell lines were chosen as model systems for cancer and normal tissue. Both cell lines consist of epithelial cells, but the cells of the MCF-7 series are carcinogenic, where the MCF-10A cells are normal growing. An algorithm is presented for distinguishing cells of the MCF-7 and MCF-10A cell lines, which has an accuracy rate of above 99%. For this purpose, two classification steps are utilized. The first step, the so-called top-level classifier searches for Raman spectra, which are measured in the nuclei region. In the second step, a wide range of discriminant models are possible and these models are compared. The classification rates are always estimated using a cross-validation and a holdout-validation procedure to ensure the ability of the routine diagnosis to work in clinical environments. Copyright © 2009 John Wiley & Sons, Ltd.