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In this study, a new microphysiological system was introduced to investigate how hypoxia affects human intestinal stem cells isolated from healthy human tissues. Both 2D and 3D expansion of hISCs were evaluated and the organoid forming efficiency was assessed using a CellRaft Array. Single cells were seeded into the Array and scanned over time to identify cells that proliferated and formed organoids. Once organoids were formed on the Arrays, longer episodes of hypoxia were evaluated to identify how it would impact hISC activity. Using the Arrays, this study identified that hypoxia primes hISCs to respond differently to interleukins than hISCs in normoxia through a transcriptional response. These findings have important implications for epithelial regeneration in the gut during inflammatory events.