The purpose of this study is to compare the in vitro cytotoxicity tests according to the ISO 10993-5 (2009) standards using direct contact and the test on liquid extracts of compounds previously identified as possible toxic impurities in perfluorocarbon liquids (PFCLs) for use in vitreoretinal surgery. Compounds including perfluorooctanoic acid (PFOA), 1H-perfluorooctane (1H-PFO), 2H-tridecafluoro-2-methylpentane, 1H,2H-octafluorocyclopentane, and 2H,3H-decafluoropentane were analyzed by 19F NMR before and after extraction using an aqueous solution and tested by both the direct contact and liquid extract tests in L929, BALB 3T3, and ARPE-12 cells. The concentration that reduced in vitro cell viability by 30%, the cytotoxicity concentration threshold (CC30), was determined for each compound. 19F NMR spectroscopy confirmed the immiscibility of perfluoro-n-octane (PFO) and 1H-PFO and the solubility of PFOA with the extraction vehicle. The other samples reacted with the extraction vehicle, releasing fluoride ions. Using the direct contact test, the CC30 of PFOA, 1H-PFO, 2H-tridecafluoro-2-methylpentane, 1H,2H-octafluorocyclopentane, and 2H,3H-decafluoropentane corresponded to 48 124, 50, 14, 8035, and 46 ppm, respectively. The method on liquid extracts did not detect cytotoxicity in three out of five tested compounds, and CC30 could not be determined. In conclusion, the in vitro cytotoxicity test by direct contact revealed a positive correlation between cell toxicity and the concentration of the tested substance. Conversely, the test on liquid extracts hardly detected the cytotoxicity of toxic impurities in PFCLs. Thus, only the cytotoxicity test by direct contact, according to ISO 10993-5 (2009), is a sensible and reliable method to detect possible cytotoxic impurities in PFCLs to guarantee patient safety.