The aim of this study is to investigate the degradation of hydrophobic coatings at the origin of reliability failure. Various properties such as adhesion and wetting after thermal ageing have been investigated. The layers studied, parylene C, Cytop and Fluoropel deposited on silicon wafers are widely used in electrowetting, MEMS and Lab-on-chip devices. A detailed failure mode analysis is presented, involving chemical surface modification through secondary ion mass spectroscopy by time of flight, X-ray photoelectron spectroscopy, surface energy and tensile strength measurements. We've been able to identify and quantify the origin of failure for each type of coating and the method we applied can be extrapolated to other hydrophobic coating as a benchmark for reliability improvement.