Derivation of naive state of mouse embryonic stem cells (mESCs) in LIF+serum (LS) culture condition is strain dependent, whereas derivation of ground state mESCs is readily possible from all strains tested so far in “2i” culture condition. ESCs can be derived from the post-implantation stage mouse embryos (EpiSCs), showing primed characteristics. In the present study, we characterized and compared the transcriptional profile of naïve, primed and ground state mESCs. Considering the importance of genetic background of mouse model for ESCs derivation in conventional culture conditions, all ESCs lines used in the study were derived from the same strain of mice. We found distinct transcriptional profiles between naive, primed and ground state mESCs. Primed state mESCs exhibit lower expression of pluripotency markers along with higher expression of lineage specific markers compared to naive and ground state mESCs. We also demonstrate that the differentiation propensity of ESCs to specific germ layer varies depending on the pluripotency state of ESCs. Overall design: Embryonic stem cells were derived from 129ola mice in naïve (LIF +serum, from pre-implanatation stage embryo ), primed (Activin A + bFGF, epiblast of E6.5 embryos) and ground state (2i+LIF and 2i+SB431542+LIF, pre-implanation stage embryo) of pluripotency. 4 lines from each condition was used for micro array analysis.