The aim of this cross-sectional study was to assess the prevalence and severity of dental anomalies according to age at cancer treatment and type of antineoplastic protocol using the Modified Dental Defect Index (MDDI) and to explore the association between MDDI scores and caries experience in Italian childhood cancer survivors (CCS). A total of 88 CCSs (age range 6-20 years) treated with chemotherapy and/or radiotherapy for malignant diseases and in remission from at least 2 years were consecutively recruited from March 2019 to July 2022. All participants were examined for dental caries and enamel defects in the permanent dentition according to the decayed-missing-filled teeth (DMFT) index and the Aine rating scale. Dental abnormalities were diagnosed using panoramic radiographs and graded for severity according to the MDDI. The MDDI values were categorized as normal (MDDI, 0), moderately abnormal (1 ≤ MDDI < 16), and severely abnormal (MDDI ≥16). None of the enrolled children had normal MDDI score. MDDI and DMFT values were higher in CCSs submitted to cancer treatment before 5 years of age, while no statistically significant association was found with anticancer protocols. A significant positive correlation emerged between DMFT and MDDI values ( p < 0.001). CCSs with moderately abnormal disturbances had statistically significant lower DMFT scores ( p < 0.001) than those with severe dental abnormalities. These findings suggest that children in remission from malignant diseases with MDDI values ≥16 have poorer dental health and should be strictly monitored by dental specialists.