PURPOSE: To analyze the efficacy of different disinfecting methods for contact lenses (CL) against Acanthamoeba castellanii (AC) using quantitative PCR (qPCR) based on RNA detection. METHODS: Three CL materials: rigid gas permeable (RGP), hydrogel (Hy), and silicone hydrogel (SiHy), were contaminated with 1x10 RESULTS: Disinfection system 1 with MS resulted in 56 % positives for RGP lenses and 100 % positives for both hydrogel materials. When MS was combined with a cleaner, 12.5 % positives were found for SiHy and 100 % negatives for Hy and RGP lenses (p <
0.05). PI solution alone yielded 38 % and 12 % positives for hydrogel and silicone hydrogel lenses, respectively, but was 100 % effective when combined with a cleaner. HP and SH, whether combined with a cleaner or not, were effective against AC for all CL materials, except HP without a cleaner for Hy lenses. CONCLUSION: All disinfection methods showed some efficacy against Acanthamoeba on any CL material. The most effective solutions were those based on hydrogen peroxide and sodium hypochlorite. Using a cleaner enhanced the final disinfecting efficacy, especially with the multipurpose solution.