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Crosslinked poly(vinyl alcohol) (PVA)/cellulose nanofibril (CNF) hybrid aerogel micro-spheres with two different particle sizes were fabricated via a combination of the water-in-oil (W/O) emulsification process and the freeze-drying process. The aerogel micro-spheres were highly porous with a bulk density as low as 0.0047 g/cm3 for the large microspheres. The pore size of the microspheres ranged from nano- to micro-meters. Preliminary biocompatibility assays of the aerogel microspheres were investigated with NIH 3T3 cells to explore their potential application as cell culture scaffolds. The highly crosslinked aerogel microspheres were robust and were able to maintain their shape during the cell culture process. The live/dead assay showed that the cells could be seeded, attached, and proliferated on the surface of PVA/CNF aerogel microspheres. The fluorescence images showed that some of the cells migrated into the inner pores of the microspheres. Moreover, the large microspheres with larger average pore sizes had a higher cell count than that of the small microspheres. This study confirms that the PVA/CNF aerogel microspheres fabricated in this work are nontoxic and biocompatible. Furthermore, the interconnected, highly porous nanofibrous structure of the microspheres can successfully facilitate cell attachment, differentiation, and proliferation.