The aim of this study was to evaluate the cytotoxicity of anti-allergic eye drops for human corneal endothelial cells (HCEC) and commercially available ocular surface cells. A primary HCEC culture was derived from human eye bank specimens. SIRC (rabbit corneal epithelium), BCE C/D-1b (bovine corneal epithelial cells), RC-1 (rabbit corneal epithelium), and Chang (human conjunctival cells) were obtained commercially. The WST-1 assay was used to measure HCEC viability, and the viability of other cells was measured using the MTT assay. Cells were treated with 7 commercially available anti-allergic eye drops for 48 h and cell viability was measured and calculated as a percentage of control. The degree of toxicity for each eye-drop solution was based on the cell viability score (CVS). HCECs treated with a 1000-fold dilution of the eye-drop solution had a viability score of 67% for Rizaben and ≥80% for the other solutions with Zepelin being the least toxic. Cell viability in response to eye-drop solutions preserved with benzalkonium chloride (BAK) was dependent on the concentration of the drug solution and exposure time. Treatment of ocular surface cells with a 20-fold dilution of the eye-drop solution resulted in the following order of cell viability as determined by their CVS: Zepelin > Ketas = Zaditen ≥ Tramelas PF = Patanol ≥ Rizaben ≥ Livostin. This order was similar to that observed for HCECs, and cell viability was found to be concentration-dependent. Based on the penetration of the drug into eye tissues, HCECs are only likely to be pharmaceutically damaging in rare cases. Epithelial cell viability depends primarily on the concentration of BAK rather than on the action of the active component in the eye-drop solution. CVS values were useful for comparison of toxicity.