The differential diagnosis of hypereosinophilia includes both primary (clonal and idiopathic) and secondary medical conditions. Here we raise the awareness of physicians to the unusual causes of hypereosinophilic states and describe the molecular assays used in the diagnosis of hypereosinophilia. Two unusual cases of hypereosinophilia in children that were initially misdiagnosed are reported. T-cell receptor gene rearrangement, skewed X inactivation, fluorescence in situ hybridization analysis, and chromosomal karyotyping were used to reach the final correct diagnosis. Both patients displayed significant eosinophilia and were initially misdiagnosed as having parasitic infection. Nonspecific T-cell clonal expansion was diagnosed in 1 patient based on the clonality of the T-cell receptor variable γ-chain and the skewed chromosome inactivation. The second patient was diagnosed with B-lineage acute lymphoblastic leukemia with a translocation (5;14) (q13;q32) that is well known to be associated with hypereosinophilia. The level of awareness to clonal expansion of WBC subsets which can cause hypereosinophilia should be high when evaluating a patient with extreme eosinophilia. Advanced molecular assays to detect clonal expansion should be used to exclude aberrant clonal processes in such patients.