This study aims to investigate the effect of culturing conditions (static and flow perfusion) on the proliferation and osteogenic differentiation of rat bone marrow (RBM) stromal cells seeded on two starch based three-dimensional scaffolds exhibiting distinct porous structures. For this purpose, it was selected: i) a scaffold based on SEVA-C (a blend of starch with ethylene vinyl alcohol) obtained by extrusion with a blowing agent and ii) a scaffold based on SPCL (a blend of starch with polycaprolactone) obtained by a fiber bonding process. The obtained results suggest that flow perfusion culture enhances the osteogenic differentiation of RBM cells and improves their distribution in 3-D starch-based scaffolds, by improving nutrients delivery in the interior of the scaffolds and simultaneously by stimulating the seeded cells by exposing them to fluid shear forces. They also indicate that scaffold architecture and pore interconnectivity affect the homogeneity of the formed tissue.