Due to high survival rates, long-term sequelae, especially neurotoxicity, need to be considered in childhood acute leukemias. In this retrospective analysis of morphologic changes of the brain in children treated for acute leukemias, we included 94 patients (77 ALL, 17 AML; 51 male, 43 female; median age: 5 years) from a single center. We analyzed 170 cranial MRI scans (T2, FLAIR axial) for morphologic alterations of the brain and variations of the ventricular width (GDAH). In addition, the corresponding literature was reviewed. More than 50% of all patients showed cerebral pathomorphologies (CP). They were seen more often in children with ALL (55.8%), ≤ 6 years of age (60.8%), in relapse (58.8%) or after CNS irradiation (75.0%) and included white matter changes, brain atrophy, sinus vein thrombosis and ischemic events. GDAH significantly enlarged mainly in children up to 6 years, with relapse, high-risk leukemias or ALL patients. However, GDAH can normalize again. The number of intrathecal Methotrexate applications (≤12 vs. >12) showed no correlation to morphologic alterations besides a significant increase in GDAH (−0.3 vs. 0.9 mm) between the first and last follow-up MRI in ALL patients receiving >12 ith. MTX applications. The role of ith. MTX on CP needs to be further investigated and correlated to the neurocognitive outcome of children with acute leukemias.