Cerebellum is involved in higher cognitive functions and plays important roles in neurological disorders. Cerebellar injury has been detected frequently in patients with preterm birth resulting in cognitive dysfunction later in life. Maternal infection and inflammation is associated with preterm birth and in neonatal brain injury. We have previously shown that intrauterine lipopolysaccharide (LPS) exposure induces white matter injury and microglial activation in the cerebral white matter tracts of neonatal rabbits, resulting in motor deficits consistent with the clinical findings of cerebral palsy (CP). Here we investigated whether intrauterine LPS exposure induced cerebellar inflammation and functional impairment. Timed-pregnant New Zealand white rabbits underwent a laparotomy on gestational day 28 (G28) and LPS (3200 EU, endotoxin group) was injected along the wall of the uterus as previously described. Controls did not receive surgical intervention. Kits born to control and endotoxin treated dams were euthanized on postnatal day (PND)1 (3 days post-injury) or PND5 (7 days post-injury) and cerebellum evaluated for presence of inflammation. The microglial morphology in cerebellar white matter areas was analyzed using Neurolucida and Neurolucida Explorer. mRNA expression of inflammatory cytokines was quantified by real-time-PCR. We found that intrauterine exposure to LPS induced intensive microglial activation in cerebellar white matter areas, as evidenced by increased numbers of activated microglia and morphological changes (amoeboid soma and retracted processes) that was accompanied by significant increases in pro-inflammatory cytokines. The Purkinje cell layer was less developed in endotoxin exposed kits than healthy controls. In kits that survived to PND 60, soma size and cell density of Purkinje cells were significantly decreased in endotoxin exposed kits compared to controls. The findings of altered Purkinje cell morphology were consistent with impaired cerebellar function as tested by eye-blink conditioning at 1 month of age. The results indicate that the cerebellum is vulnerable to perinatal insults and that therapies targeting cerebellar inflammation and injury may help in improving outcomes and function.