Infants and very young children with malignant brain tumors usually have unfavourable locations and are not candidates for craniospinal irradiation. New therapeutic approaches must be attempted to improve poor survival rates. The primary goal of the present study was to report on the safety profile and toxicity of intrathecal administration of liposomal cytarabine in children <4 years with malignant brain tumors. This is the first study including this group of patients receiving intrathecal liposomal cytarabine. Nine patients with a median age of 26 months were eligible for the study. The diagnoses were ependymoma (3), peripheral neuroectodermic tumor (PNET) (2), meduloblastoma, atypical teratoid rhabdoid tumor (ATRT), cerebral lymphoma, and rhabdomyosarcoma with CNS invasion. Liposomal cytarabine at doses between 20 and 35 mg were administered by lumbar puncture. Dexamethasone was given for arachnoiditis prophylaxis. A total of 44 doses (median = 6) of liposomal cytarabine were administered. Neurological side effects possibly related to liposomal cytarabine were observed in five patients (55.6%). This incidence was higher than previously reported in children older than 3 years. Eight of the patients (89%) experienced an initial improvement of clinical symptoms after initiation treatment, confirmed by MRI. This study demonstrates the feasibility of using intrathecal liposomal cytarabine in children under 4 years of age with malignant brain tumors.