Purpose To compare the cytotoxicity of different fluoroquinolones (FQs) towards human corneal epithelial cells (HCECs). Methods HCECs were incubated with FQs (norfloxacin, ciprofloxacin, ofloxacin, levofloxacin, moxifloxacin, and gatifloxacin), both as commercial ophthalmic formulations and as unpreserved solutions. Cells incubated in different formulations of gentamicin, cefazolin, and benzalkonium chloride (BAC) were also compared. A cell viability assay, using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay, was used to evaluate the drug effects on cell viability after five incubation times (30 min, 1 h, 4 h, 8 h, and 24 h). Transepithelial electrical resistance (TEER) was measured with a voltohmmeter to help understand changes in paracellular permeability at five time points (4 h, 8 h, 12 h, 24 h, and 48 h). Cell morphology was observed with an inverted fluorescence microscope, with multiple stage position and in time-lapse mode. Results The preserving solutions and BAC at concentrations above 0.005% significantly decreased cell viability, when assayed by MTS. Increased paracellular permeability and decreased membrane integrity were also observed by TEER measurements and inverted fluorescence microscopy. Ofloxacin and levofloxacin were both free of preservatives and showed the least cytotoxicity towards HCECs in commercial FQ eye drops. Conclusions The cytotoxicity observed with FQ eye drops seems to be caused mainly by the preservative, which induced a significant decrease in membrane integrity and increased paracellular permeability. We found the new generation of FQs (moxifloxacin and gatifloxacin) no less cytotoxic towards HCECs than the old generation ones.