The vertebrate early stage embryo is consisting of the three primary germ layers ectoderm, mesoderm and endoderm, from which all organ tissues are developed. During early embryonic development, mesodermal cells become sequentially determined to more precisely defined cell types including muscle, heart, vasculature, blood, kidney, gonads, dermis and cartilage. How the prospective mesodermal cells integrate the various signals they receive and how they resolve this information to regulate their morphogenetic behavior and cell fate decisions is largely unknown. Understanding of this complex phenomenon is essential to induce selective differentiation of pluripotent stem cells into clinically relevant, physiologically functional cells such as cardiomyocytes or for transdifferentiation of easily accessible cell types such as fibroblasts into other clinically relevant cell types for applications such as cell replacement therapy, accelerated drug discovery and drug toxicological testing. This demands an in-depth analysis of the mesodermal endogenous signaling cascades and transcription factor networks. Emerging results from isolation and transcriptome characterization of pure mesodermal cells derived from murine embryonic stem cells define the genetic and cellular identity of mesodermal cells and allows a comprehensive analysis of the very dynamic process of mesodermal patterning which would not be technically feasible with conventional embryology methods.This review focuses on defining the transcriptomic signatures of mesodermal cells and their lineages with special reference to the molecular and signaling pathways associated with the complex process of mesodermal patterning.