We have recently developed new 3D hydroxyapatite/collagen (50/50 wt%) scaffolds using a biomimetic synthesis approach. The first in vitro tests performed in static culture showed a limited cell colonization and survival inside the scaffolds. The current study evaluated in dynamic culture the scaffold changes and colonization by human immortalized osteoprogenitor STRO-1A cells. The stability of our scaffolds in the different culture conditions (static, low flow, high flow) was validated by the maintenance of the pore diameter and interconnectivity over 21 d. The colonization and the viability of STRO-1A cells inside the scaffolds were further evaluated on histological sections. It was demonstrated that only the high flow-rate allowed cell survival after 7 d and a complete scaffold colonization. Moreover, the colonization and viability were different in function of the scaffold position inside the perfusion container. The differentiation markers (alkaline phosphatase activity, type I procollagen and osteocalcin synthesis) of STRO-1A cells were analyzed in the culture medium after 7, 14 and 21 d. The low flow-rate increased significantly the three markers compared with static conditions. In contrast, markers were reduced in high flow-rate compared with low flow-rate. To explain this surprising result, we hypothesized that the different molecules were actually adsorbed on the scaffold because of the closed circuit used in the high flow-rate conditions. In summary, this study provides original results on the influence of flow rate but mostly of the circuit used (open/closed) on the structural modifications and cell colonization of collagen-HA scaffolds.