Epidemiological studies suggest that early life infections may contribute to the development of neuropsychiatric disorders later in life. Experimental studies employing infections during neonatal life support this notion by reporting persistent changes in the behaviour of adult animals, including deficits in sensorimotor gating. We have previously described an induction of the kynurenine pathway in neonatal wild-type (WT) mice following a systemic infection with neurotropic influenza A/WSN/33 virus. Here, we use the same model of infection in both WT and Tap1-/- mice (expressing reduced levels of MHC class I) and study long-term effects of the infection on sensorimotor gating, as determined by measuring prepulse inhibition (PPI). Moreover, transcription of genes encoding enzymes in the kynurenine pathway and levels of kynurenic acid (KYNA), in the brain of Tap1-/- mice were investigated. In mice infected on postnatal day (P)3 or P4, the levels of several transcripts in the kynurenine pathway were altered at P7, P13 and P24. Transcripts encoding indoleamine-pyrrole 2,3-dioxygenase (IDO), degrading tryptophan in the first step of the kynurenine pathway were consistently up-regulated at all time-points investigated. The changes in transcript levels were accompanied by a transient elevation of KYNA in the brain of infected mice at P13. At age 5-6 months, neonatally infected Tap1-/-, but not WT, mice exhibited a reduction in PPI. The present data show that a neonatal infection targeting the brain can induce the kynurenine pathway and that such an infection can disrupt sensorimotor gating in adulthood in genetically vulnerable mice.