Both BTK-deficient and sufficient iPSCs successfully differentiated and expressed TMEM119, TREM2, and IBA1. BTK-deficient iMicroglia were smaller and tended to cluster. Using a zymosan-based phagocytosis assay as a screening tool to evaluate phagocytosis in microglia, we found that BTK-deficient iMicroglia had reduced phagocytosis compared to controls. To assess cytokine production, BTK-sufficient and BTK-deficient iMicroglia were stimulated with LPS and supernatant cytokine levels were measured using a 47-plex Luminex assay. The results showed a significant reduction in pro-inflammatory cytokines (IL-6, TNF-α and IL-1β) and type I (IFNα) interferon in BTK-deficient microglia. Furthermore, chemokines associated with Th1/Tc1 responses, including CXCL10 (IP-10) and CCL2 (MCP-1), were markedly decreased, whereas CCL22 (MDC), a chemokine that promotes Th2/Tc2 response, was significantly elevated.