In this study, dynamic mechanical thermal analysis was used to evaluate the changes that occurred in maxillofacial elastomers subjected to different disinfecting regimens. A commercial polydimethyl siloxane (PDMS) and an experimental chlorinated polyethylene (CPE) were treated with different disinfection procedures for a period that simulates 1 year of clinical service: microwave exposure (D1), hypochlorite solution (D2), neutral soap (D3), and a commercial disinfecting solution (D4). A fifth group was kept in dark storage as control. Dynamic mechanical thermal analysis tests operated in a fixed frequency (1 Hz) over a range of temperatures (-130°C to 20°C for PDMS, -60°C to 120°C for CPE). Loss modulus (G″), storage modulus (G'), and loss factor (tanδ) were recorded as a function of temperature. The obtained glass transition temperature (Tg) values were subjected to statistical analysis. Dynamic mechanical thermal analysis revealed changes in Tg values for both materials, which reflect the possible changes in their chemical and physical structure, after different disinfection procedures. The PDMS and CPE samples seem to have less dense structure maybe because of chain scission reaction that probably occurred during the disinfection procedures. According to statistical analysis, Tg values presented significant changes from the control samples among the different materials and disinfecting procedures. Microwave exposure and hypochlorite solution affect CPE significantly, whereas PDMS exhibited significant changes after being treated with a commercial antimicrobial agent, concerning changes that occurred in Tg. In all cases, Tg values were decreased compared with the untreated samples, which were stiffer, presenting higher Tg and G' values.