Detected kidney stone cases are increasing globally, yet knowledge on the conditions for stone formation is lacking. Experimental approaches mimicking the micro-environmental conditions present in vivo can help sci-entists untangle intertwined physiochemical and biological phenomena leading to kidney stone formation. As crystal nucleation often initiates at liquid-solid interfaces, the interface morphology plays a significant role in the rate of nucleation. Within the nephron, the functional unit of the kidney, four segments can be distinguished that contain different surface morphologies. Particularly, the cells lining these segments contain protrusions in the shape of nanopillars that vary in length, diameter and spacing. Exploiting the opportunities provided by organ- on-a-chip technology, we designed and manufactured a proof-of-principle microfluidic device proposed to in-crease our understanding of the relation between kidney surface morphology and kidney stone crystallization. We used two-photon polymerization to fabricate biocompatible surfaces that mimic the nephron morphologies with materials properties similar to those of biological structures. The fabricated cilia were incorporated in the microfluidic device, which was designed to observe in vitro crystallization of calcium oxalate under flow@en