Progress in the field of mitochondrial biology in the past few years has shown that mitochondrial activities go beyond bioenergetics. These new aspects of mitochondrial physiology and pathophysiology have important implications for the immature brain. A picture emerges in which mitochondrial biogenesis, mitophagy, migration, and morphogenesis are crucial for brain development and synaptic pruning, and play a part in recovery after acute insults. Mitochondria also affect brain susceptibility to injury, and mitochondria-directed interventions can make the immature brain highly resistant to acute injury. Finally, the mitochondrion is a platform for innate immunity, contributes to inflammation in response to infection and acute damage, and participates in antiviral and antibacterial defence. Understanding of these new aspects of mitochondrial function will provide insights into brain development and neurological disease, and enable discovery and development of new strategies for treatment.