The flow in a micro-mixer based on artificial cilia (J. M. J. den Toonder, F. M. Bos, D. J. Broer, L. Filippini, M. Gillies, J. de Goede, G. N. Mol, M. Reijme, W. Talen, J. T. A. Wilderbeek, V. Khatavkar and P. D. Anderson, Lab Chip, 2008, 8, 533–541) is studied. A numerical model is developed and simulations are performed for Reynolds numbers (Re), based on the cilium dimension, from 0 to 10. The mixing properties of the flow are investigated both quantitatively and qualitatively. Flow visualisation by optical coherence tomography (OCT) is performed, and experimental and numerical particle distributions are compared. It is found that for higher Reynolds numbers (Re > 0.1) inertial effects cause a flow reversal compared to lower Reynolds numbers (Re < 0.1). Flow inertia also results in a significant increase of the distributive mixing. The qualitative agreement between experiments and simulations at higher Re is good. This indicates that local inertia effects play a key role in the mixing effectiveness of the artificial cilia mixing.