Although cellular metabolism of pluripotent stem cells is still largely unexplored, metabolomics is a promising approach for a fast identification of stem cells during the differentiation process. In this paper we report the first investigation of the volatile compounds released by pluripotent stem cells respect to the differentiation to floating and adhesion embryonic bodies and to early neural progenitors. Gas chromatographic analysis shown a pattern of 20 volatile compounds specific for each step of the differentiation process. Gas chromatographic analysis have been corroborated by those obtained with an array of metalloporphyrins coated quartz microbalances.