Podophyllum hexandrum Royle (=Sinopodophyllum hexandrum) is a high-altitude medicinal plant exploited for its etoposides which are potential anticancer compounds. An effective, conventional propagation method is by seed. However, seed germination is erratic, and seedling survival is low. A marginal increase in Podophyllum seed germination was attained with organic solvents. In the present study an attempt was made to decipher the physiological and biochemical barriers in terms of change in proteins during seed germination of Podophyllum. Comparative 2-DE analysis between un-germinated (dormant) and germinating seeds revealed nearly 113 differentially expressed proteins, whereas Peptide Mass Fingerprint (PMF) analysis of 97 protein spots revealed appearance of 27 proteins, up-accumulation of 11 proteins, down-accumulation of 19 proteins and disappearance of 40 proteins with germination. Identified 59 proteins in the homology search were involved in metabolism (carbohydrate and amino acid metabolism; 20 proteins), ABA/GA signaling (17 proteins) and stress (15 proteins) related proteins. Seven proteins were with unknown function. Two-DE, and MS/MS analysis in conjunction with semi-quantitative RT-PCR data of cell wall hydrolyzing genes, revealed that in Podophyllum the radicle protrusion occurs might be because of the up-accumulation of cell wall hydrolases i.e. β-1, 3-glucanase and XET which weakens the thick walled micropylar endosperm.