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In this paper, natural convection heat transfer inside an enclosure which is partially filled with porous layer is reported using lattice Boltzmann method. Generalized equations in modeling flow in porous media have been employed which are coupled with the lattice Boltzmann formulation of the momentum and energy equations. The present study investigates the effect of position of porous layer on heat transfer rate for different dimensionless parameters, such as Rayleigh number, Darcy number and porosity of the porous layer. In addition, a modified Rayleigh number is presented as an effective parameter which affects the degree of penetration of the fluid into the porous layers. The obtained results showed that the heat transfer rate in the case of vertical layer is more than that of horizontal porous layers.