Abstract Background Emerging genetic studies of late‐onset Alzheimer’s Disease (LOAD) implicate microglia, the brain’s resident macrophages. More than half the risk genes associated with LOAD are expressed in microglia, yet we know little about the underlying biology or how myeloid cells contribute to LOAD pathogenesis. Single‐cell transcriptomic studies reveal diverse microglial states in patients and mouse models; however, we lack tools to track these states and understand the impact of environmental challenges or genetic susceptibility. Method We used human embryonic and induced pluripotent stem cell models to gain insights into microglia. These cells can be differentiated into microglia, enabling the broad characterization of cells in vitro and understanding their impact on the other cell types in xenograft models, allowing us to gain biological insight into disease pathogenesis. Result Our lab has developed a novel human stem cell‐based platform1 which induces stem cell‐derived microglia (iMGLs) to take on diverse transcriptional signatures similar to those found in the human brain in response to exposure to brain‐relevant substrates. Moreover, we conceived a lentiviral protocol that allows for efficient genetic manipulation of microglia (>90% transduction). Building on these systems, we generated reporters of microglia state to track the expression of key microglial genes and adapted iPSC “villages”2, or pooled cultures, that combine iPSC cell lines in the same dish. Using these tools in vitro and in xenograft models3,4, we identified genetic regulators and functional changes of microglia states in LOAD. Conclusion Together, these tools represent a broad toolset that will allow us to answer some of the most pressing questions, such as when and how in disease these states are formed, what is their impact on disease progression, and how plastic they are. These tools will be invaluable to understanding the role of microglia in AD and the brain in general. 1. Dolan, M.‐J. et al. Biorxiv 2022.05.02.490100 (2022) 2. Wells, M. F. et al. Biorxiv 2021.11.08.467815 (2021) 3. Hasselmann, J. et al. Neuron 103 , 1016‐1033.e10 (2019) 4. Mancuso, R. et al. Nature Neuroscience 22 , 2111‐2116 (2019)