Ischemic stroke is an important cause of death and long term morbidity in children. Viral respiratory infections are emerging as important risk factors responsible for ischemic stroke in this age group. The direct action of virus against cerebral vessels, autoimmune reactivity, and increased production of cytokines are advocated as the main factors for causing ischemic stroke. This study can be useful for clarifying some molecular aspects of H1N1 virus infection in children. We report on the case of a H1N1-induced ischemic stroke in a Caucasian 2 year-old female. The cerebrospinal fluid samples showed the positivity of polymerase chain reaction for influenza A (H1N1) infection, confirmed also by pharyngeal swab culture. Increased levels of cerebrospinal fluid interleukin 6 and interleukin 1β were also detected. H1N1 virus infection has been identified as an important cause of neurological involvement in children. The findings of increased levels of Interleukin 6 and interleukin 1β in the cerebrospinal fluid of this child with H1N1 induced-ischemic stroke seems to validate the role of pro-inflammatory cytokines as crucial mediators of cerebral thrombus formation.