The aim of the study was to examine the influence of different antibiotics on amniotic membrane epithelium and to observe the related ultrastructural changes using transmission electron microscope (TEM). Prospective comparative laboratory study. Amniotic membrane samples from a single placenta were obtained using a sterilized method. Tissue samples were placed in either saline or antibiotics-containing (penicillin, streptomycin, neomycin, or amphotericin B) solutions. The viability of the amniotic membrane epithelial cells was then assessed for saline and antibiotics using both light microscope and TEM to investigate morphological changes. The ultrastructural examination of amniotic membrane epithelium held in antibiotics-containing solutions showed damage to the cell membrane, rarefaction, and loss of microvilli. Amniotic membrane from the control group showed intact epithelium, with surface microvilli and junctional complexes between the cells and the basal membrane. The destructive effects of antibiotics on freshly obtained amniotic membrane were examined with both light microscopy and transmission electron microscopy and significant differences in the ultrastructure were observed.