Alzheimer’s disease (AD) is a neurodegenerative disease characterised by amyloid plaques and neurofibrillary tangles that progressively leads to loss of cognition. A small percentage of cases are described as familial or early-onset AD (EOAD) and are caused by mutations in genes, including amyloid precursor protein (APP) gene duplication or loss of function mutations in proteins that process APP, presenilin 1 or 2 (PSEN1, PSEN2). The vast majority of cases are late-onset (LOAD) and are affected by multiple genetic and environmental risk factors. A major genetic risk factor for LOAD is the APOE4 genotype but the precise role of APOE in AD pathogenesis remains hotly debated [1]. For decades models of AD have focused on EOAD gene mutations, even though the disease mechanisms for EOAD and LOAD are likely distinct. APOE is highly expressed in microglia and it is hypothesised may play a role in AD pathogenesis via altering microglial function. However it is unclear whether the EOAD mutations also affect microglial function. We developed a high-yield protocol for producing human microglia-like cells (iMGs) from induced pluripotent stem cells (iPSCs) that express microglial signature genes and functional responses. We generated iPSC lines from LOAD and EOAD patients, healthy individuals and isogenic controls to assess EOAD mutations and APOE genotype on microglial gene expression and function. We identified that the APOE4 genotype has a profound impact on several aspects of microglial functionality whereas EOAD mutations led to only minor alterations. Our data shows that EOAD mutations and the APOE4 phenotype confer disparate phenotypes in human iPSC-derived microglia and suggest that the role of microglia in disease pathogenesis may be distinct in EOAD versus LOAD.