This paper proposes a new level set-based topology optimization method for thermal problems that deal with generic heat transfer boundaries including design-dependent boundary conditions, based on the level set method and the concept of the phase field theory. First, a topology optimization method using a level set model incorporating a fictitious interface energy derived from the concept of the phase field theory is briefly discussed. Next, a generic optimization problem for thermal problems is formulated based on the concept of total potential energy. An optimization algorithm that uses the Finite Element Method when solving the equilibrium equation and updating the level set function is then constructed. Finally, several three-dimensional numerical examples are provided to confirm the utility and validity of the proposed topology optimization method. Copyright © 2009 by ASME.