With the development of high-throughput technologies like microarrays for genomic and transcriptomic analysis, and two-dimensional gel electrophoresis, mass spectrometry, and protein arrays for proteomic analysis, it is possible to monitor the changes in gene or protein expression of several hundreds, or even thousands of molecules simultaneously. Within the last years, these technologies have been applied successfully to stem cell research. One of the aims of stem cell expression profiling is to find specific marker genes or proteins which may determine the "stemness" of these cells. In the current review, we will evaluate the results of genomic, transcriptomic and proteomic approaches to find stem cell markers. We compare the criteria of "stemness" to recent results in adult neural stem cell research. Neural stem cells have been isolated from various regions of the adult brain. They self-renew and give rise to progeny capable to generate neurons, astrocytes, and oligodendrocytes. Besides morphological differentiation, these cells can integrate into functional neuronal circuits, making them suitable targets for cell replacement strategies. General properties seem to be the responsiveness to growth factors, and the activation of developmental signaling pathways. In conclusion, we suggest that stem cell properties can be specified by global gene or proteomic expression patterns rather than by the analysis of individual genes or proteins.