In order to achieve functional tissue with the correct biomechanical properties it is critical to stimulate mechanically the cells. Perfusion bioreactor induces fluid shear stress that has been well characterized for two-dimensional culture where both simulation and experimental data are available. However these results can't be directly translated to tissue engineering that makes use of complex three-dimensional porous scaffold. Moreover, stimulated cells produce extensive extra-cellular matrix (ECM) that alter dramatically the micro-architecture of the constructs, changing the local flow dynamic. In this study a Fourier domain Doppler optical coherent tomography (FD-DOCT) system working at 1300nm with a bandwidth of 50nm has been used to determine the local flow rate inside different types of porous scaffolds used in tissue engineering. Local flow rates can then be linearly related, for Newtonian fluid, to the fluid shear stress occurring on the pores wall. Porous chitosan scaffolds (φ1.5mm × 3mm) with and without a central 250 um microchannel have been produced by a freeze-drying technique. This techniques allow us to determine the actual shear stress applied to the cells and to optimise the input flow rate consequently, but also to relate the change of the flow distribution to the amount of ECM production allowing the monitoring of tissue formation.