The study aimed to assess the diagnostic accuracy of Flow cytometry (FCM) immunophenotyping and IgH gene rearrangements (IGHRs) by real-time PCR in comparison with classic cytology for diagnosing CNS infiltration in pediatric ALL. We concluded that the diagnostic value of FCM and IGHR are two to three times more than that of cytology. Therefore, immunophenotyping by FCM is recommended for routine diagnosis of CSF infiltration. Furthermore, IGHR analysis by real-time PCR appears to be a useful addition in evaluation of CNS infiltration.