Since, a protein complex can be considered as a minimal biological structure of a cellular compartment , complexomic study of human embryonic stem cells and human embryonic carcinoma cell has been done for the first time via Blue native polyacrylamide gel electrophoresis (BN-PAGE) following by denaturing SDS-PAGE. Membrane and cytosolic fractions of hESC(Royan H5) and hECC(N-Tra2) has been prepared and the reliability of the fractionation has been confirmed by western blotting with utilization of membrane and cytosolic markers. More than 70 membrane proteins and about 100 cytosolic ones from BN-PAGE proteome maps were identified using MALDI TOF/TOF. Different possible protein complexes were validated by computational prediction of possible protein-protein interactions according to STRING databank and confirmed protein complexes based on the molecular weight of complex estimated by BN PAGE and STRING results introduced as Cytosolic Protein Complex (CPC) and Membrane Protein Complex (MPC) and also homooligomers. Database search revealed many attractive results about protein complexes and active metabolic pathways in both hESC and hECC.