Electrophoretic protein profiles were used in this study as a successful tool to estimate the possible mutagenic potentialities produced by the possible genotoxic effect Ethyle methane sulphonate ., Endoxan and its relation to the variations induced in mitotic index . This work aimed to study the relation between protein banding patterns and mitotic index in  Allium cepa, L . root tip cells treated with three concentrations from each of EMS and Endoxan. The results appeared that there was a progressive decrease in protein synthesis of 16 out from 18 bands obtained from electrophoretic patterns .Protein biosynthesis was markedly affected by EMS than Endoxan as shown in bands intensity and mitotic index in EMS treatments compared with Endoxan. This indicated that the intensity of protein bands was related to mitotic index. Both chemical agents disappeared the band number five at high molecular weight region, which could be attributed to the deletion of their corresponding genes  In contrast , the intensity of one band ( band number 4 , which having a MW 72 KDa ) was stable and did not affected by any of both chemical agents which were  used in this study . Negative correlation value (-0.25) was obtained between the relative front and the molecular weight of bands. The results revealed positive correlation between mitotic index and protein intensity affected by EMS and Endoxan. The results indicated that EMS and Endoxan were markedly effective on the level of gene expression as shown from the intensity of bands obtained herein. Thus, electrophoretic technique of protein patterns have been used as a successeful tool to estimate the possible mutagenic potentialities induced by EMS and Endoxan via  variations induced in protein intensity .