Nature Reviews Neuroscience, Published online: 20 July 2026; doi:10.1038/s41583-026-01066-w Transcriptomic microglial states are shaped by development, ageing, genetics, environment and disease. In this Review, Eggen and Kooistra discuss how the formation of so-called hidden immune-memory states in microglia following stimulus exposure might contribute to the variability in neurological disease outcomes.