Microglia, mainly known for their role in innate immunity and modulation of neuroinflammation, play an active role in central nervous system development and homeostasis. Depending on the context and environmental stimuli, microglia adopt a broad spectrum of activation status from pro-inflammatory, associated with neurotoxicity, to anti-inflammatory linked to neuroprotection. Pro-inflammatory microglial activation is a key hallmark of white matter injury in preterm infants and is involved in developmental origin of adult neurological diseases. Characterization of neonatal microglia function in brain development and inflammation has allowed the investigation of promising therapeutic targets with potential long-lasting neuroprotective effects. True prevention of neuro-degenerative diseases might eventually occur as early as the perinatal period.