Hydrogels are increasingly used as a surrogate extracellular matrix in three-dimensional cell culture systems, including microfluidic cell culture. Matrigel is a hydrogel of natural origin widely used in cell culture, particularly in the culture of stem cell-derived cell lines. The use of Matrigel as a surrogate extracellular matrix in microfluidic systems is challenging due to its biochemical, biophysical, and biomechanical properties. Therefore, understanding and characterising these properties is a prerequisite for optimal use of Matrigel in microfluidic systems. We used rheological measurements and particle image velocimetry to characterise the fluid flow dynamics of liquefied Matrigel during loading into a three-dimensional microfluidic cell culture device. Using fluorescence microscopy and fluorescent beads for particle image velocimetry measurements (velocity profiles) in combination with classical rheological measurements of Matrigel (viscosity versus shear rate), we characterised the shear rates experienced by cells in a microfluidic device for three-dimensional cell culture. This study provides a better understanding of the mechanical stress experienced by cells, during seeding of a mixture of hydrogel and cells, into three-dimensional microfluidic cell culture devices. (C) 2018 Author(s)