Due to antibacterial characteristic, amnion has been frequently used in different clinical situations. Developing an in vitro method to augment endogenous antibacterial ingredient of amniotic epithelial and mesenchymal stem cells is desirable for a higher efficacy of this promising biomaterial. In this study, epithelial or mesenchymal side dependent effect of amniotic membrane (AM) on antibacterial activity against some laboratory and clinical isolated strains was investigated by modified disk diffusion method and colony count assay. The effect of exposure to IL-1β in production and release of antibacterial ingredients was investigated by ELISA assay. The results showed that there is no significant difference between epithelial and mesenchymal sides of amnion in inhibition of bacterial growth. Although the results of disk diffusion showed that the AM inhibitory effect depends on bacterial genus and strain, colony count assay showed that the extract of AM inhibits all investigated bacterial strains. The exposure of AM to IL-1β leads to a higher level of antibacterial peptides secretion including elafin, HBD-2, HBD-3 and cathelicidic LL-37. Based on these results, amniotic cells possess antibacterial activity which can be augmented by inflammatory signal inducers; a process which make amnion and its epithelial and mesenchymal stem cells more suitable for tissue engineering and regenerative medicine.