New applications involving aerosol transport in microscale configurations requires the derivation of the penetration efficiency of aerosols in microchannels. Although many analytical solutions for the aerosol penetration in channels have been investigated, none of them are applicable for microchannels. Previously, the no-slip condition for the gas velocity and the zero particle concentration boundary condition have been applied to the convection diffusion equation. However, recent studies show these boundary conditions may not be appropriate for microscale geometries. The particle penetration through rectangular microchannels and cylindrical microtubes has been obtained using the numerical Crank Nicolson method with slip flow at the walls. Existing correlations for the aerosol penetration have been modified for the slip flow regime based on an optimization method. These correlations give the penetration as a function of the dimensionless deposition factor and Knudsen number of the gas. At large Knudsen numbers the penetration decreases relative to the case with continuum flow. Therefore, the aerosol penetration decreases in the slip flow regime. However, the non-zero boundary condition for the particle concentration at the walls does not have any significant effect on the model results of the particle penetration. 2011 (C) Elsevier Ltd. All rights reserved.