The infection of the pregnant female and the ensuing induction of maternal immune activation affect fetal development with long-lasting consequences for health and disease. Specifically aberrant neural wiring may contribute in the manifestation of psychiatric disorders such as depression. Here, we investigated altered resting state functional connectivity using fMRI in adult mice after prenatal immune activation. While the overall flow of information was intact, especially the cortico-limbic connectivity was disrupted in resting state networks of adult offspring. We propose that these altered connectivity patterns may lead to behavioral and emotional abnormalities with relevance for neuropsychiatric disorders.