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Polymer optical waveguides are viewed as a potential interconnect solution in board-level optoelectronic systems. In this paper, the optical loss changes in siloxane polymer waveguides during thermal aging conditions are studied for the wavelengths of 850 and 1310 nm. The optical loss in waveguides during intended operation and temperature exposure can increase due to factors such as oxidation of waveguides, increased absorption, and scattering. In addition to these inherent changes in the optical properties of the waveguides, physical failures such as delamination and cracking of waveguides will also increase the optical loss. This paper focuses on the first set of parameters that affects the optical loss and as a first step; the optical absorption of the polymer material is characterized through spectroscopy experiments. The thermal-aging dependent optical loss is determined for waveguide samples at several different accelerated temperature conditions. The temperature contours in a polymer waveguide with an embedded laser are determined from experiments as well as finite-element modeling. Using experimental data, analytical models have been developed that relate the optical loss with temperature and time, and provide a practical way of determining the reliability of the optical waveguides during field-use conditions.