In this work, various three-dimensional (3D) scaffolds were produced via microstereolithography (m-SLA) and 3D printing (3DP) techniques. This work demonstrates the advantages and disadvantages of these two different rapid prototyping methods for production of bone scaffolds. Compared to 3DP, SLA provides for smaller feature production with better dimensional resolution and accuracy. The permeability of these structures was evaluated experimentally and via numerical simulation utilizing a newly derived Kozeny– Carman based equation for intrinsic permeability. Both experimental and simulation studies took account of porosity percentage, pore size, and pore geometry. Porosity content was varied from 30% to 70%, pore size from 0.34 mm to 3 mm, and pore geometries of cubic and hexagonal closed packed were examined. Two different fluid viscosity levels of 1 mPas and 3.6 mPas were used. The experimental and theoretical results indicated that permeability increased when larger pore size, increased fluid viscosity, and higher percentage porosity were utilized, with highest to lowest degree of significance following the same order. Higher viscosity was found to result in permeabilities 2.2 to 3.3 times higher than for water. This latter result was found to be independent of pore morphology type. As well as demonstrating method for determining design parameters most beneficial for scaffold structure design, the results also illustrate how the variations in patient’s blood viscosity can be extremely important in allowing for permeability through the bone and scaffold structures.