Eukaryotes (such as yeasts) and prokaryotes (such as bacteria) differ in size, molecular complexity, etc. By definition, eukaryotic cells store their DNA in a separate internal compartment, the so-called nucleus. Owing to this molecular compartmentalization, the identification of yeast cells by vibrational spectroscopy at a single-cell level is challenging. This contribution reports on first results of micro-Raman analysis together with a hierarchical cluster analysis allowing for an online identification method for yeast cells at a single-cell level. For the classification analysis, an average spectrum from 10 different measuring points within a single yeast cell was used to overcome the heterogeneity of the yeast cells. Copyright (c) 2005 John Wiley & Sons, Ltd.