In this study, heat transfer and aerosol deposition in the under-floor and Baseboard heating systems have been investigated, numerically. The aim of this study is a comparison between these heating systems. This comparison obtains the optimal heating system with low suspended particles in the air. Computational fluid dynamic with Eulerian-Lagrangian method has been used to simulate fluid and particles flows. The velocity and temperature distribution have been obtained by solving the equations of continuity, momentum and energy. It is resulted that, the radiant heat transfer contains about 63 % and 60 % of overall heat transfer of the under-floor and Baseboard heating systems, respectively. Side walls have a same condition for deposing the particles in both of investigated heating systems, approximately. But, in floor heating system, most of the particles are deposited under the roof, while the Baseboard heating system has a more percentage of seated particles on the floor.