Laboratory evaluation of patients with suspected systemic mastocytosis (SM) includes: (1) morphologic review of bone marrow biopsies and aspirates, (2) molecular testing for the presence of the KIT mutation and (3) immunophenotypic analysis of mast cells and other hematopoietic elements by flow cytometry. Recently, we have developed RT-PCR/RFLP assay for detection of the most prevalent KIT mutation in mastocytosis patients (D816V).The KIT D816V mutation results in constitutive activation of the receptor tyrosine kinase and is believed to be involved in disease pathogenesis. We have also developed a flow cytometric assay for immunophenotypic analysis of mast cells, since it has been recently described that neoplastic mast cells display aberrant immunophenotype, most notably, aberrantly coexpress CD117 with CD25 and/or CD2. Aberrant expression of CD25 and CD2 is not detected in normal marrow mast cells. The identification of the KIT D816V mutation in patients with systemic mastocytosis has lately gained a major prognostic significance, largely because of the availability of tyrosine kinase receptor inhibitors such as imatinib. Imatinib was shown to be ineffective in patients carrying KIT D816V mutation, but effective in cases with some other mutations. For example, the FIP1L1/PDGFRA fusion kinase is inhibited by imatinib. Therefore, it is of paramount importance to correctly identify SM patients with KIT D816V mutation because of differences in clinical sequelae, prognoses and selection of treatment. Detection of other molecular/cytogenetic abnormalities in SM patients is infrequent. We identified an unusual case of a patient presenting with peripheral basophilia and systemic mastocytosis in whom cytogenetic analysis revealed a t(4;5)(q21.1;q31.3). Translocations involving region 5q31-32 (PDGFRB) have been reported in a variety of myeloproliferative diseases and are often associated with significant peripheral eosinophilia. We used molecular analysis to determine the role of PDGFRB in this case. Fluorescence in situ hybridization (FISH) documented a breakpoint in PDGFRB. In agreement with this, the patient responded very well to imatinib treatment with resolution of clinical symptoms, basophilia, and mast cell disease. Molecular analysis revealed that PDGFRB, encoding an imatinib-sensitive tyrosine kinase, was fused to PRKG2. The fusion gene incorporates the first two exons of PRKG2 fused to the truncated exon 12 of PDGFRB, resulting in the disruption of its juxtamembrane domain. Functional studies confirmed that the activity and transforming properties of PRKG2-PDGFRbeta were dependent on the disruption of the auto-inhibitory juxtamembrane domain. Our results identify a second case of the PRKG2-PDGFRB fusion and confirm the unusual PDGFRB breakpoint associated with this fusion. This work also illustrates the use of imatinib for the treatment of specific cases of systemic mastocytosis. Pediatric onset mastocytosis usually presents as urticaria pigmentosa; and less often as diffuse cutaneous mastocytosis. While the literature indicates that disease often resolves, there has been a move to more aggressive therapy for mastocytosis early in life. We addressed the long term prognosis of pediatric-onset disease by examining 17 children with mastocytosis which we had reported on in 1989. We successfully contacted 15 of these patients and data was collected regarding their clinical status. Original bone marrow specimens were re-stained, re-examined, and correlated with disease outcome using consensus criteria. Three of five patients with persistent disease underwent repeat bone marrow biopsies. Results showed that there was complete regression of disease as defined by cutaneous findings and symptoms (clinical disease severity) in 10 of 15 patients (67%). Three patients had major (20%) and two had partial regression of disease (13%). Repeat marrow examinations on three patients with persistent disease documented systemic mastocytosis based on marrow findings in one patient who had partial regression of disease and was the only patient with initial morphologic evidence of systemic disease. Of the remaining two patients, one demonstrated partial regression and the other major regression of disease; and neither had evidence of systemic mastocytosis. In conclusion, this study demonstrates that initial bone marrow biopsies were prognostic in that those without evidence of systemic disease experienced disease regression; and that the long term prognosis for children managed symptomatically with mastocytosis is highly encouraging.