Chronic myelogenous leukemia (CML) is characterized by the specific cytogenetic translocation t(9;22)(q34;q11.2), also called the Philadelphia (Ph) chromosome. We present a case of a cryptic BCR/ABL1 fusion, which was not originally detected by standard karyotyping. The patient is a forty-seven-year-old man who presented with leukocytosis. Bone marrow biopsy was consistent with CML in chronic phase with no increase in myeloblasts. Conventional cytogenetic studies revealed a 46,XY karyotype. Despite this finding, the patient was started on hydroxyurea therapy followed by Gleevec. At six-month follow-up, a repeat karyotype was again normal, though FISH analysis was positive for BCR/ABL1 fusion. FISH performed on previously G-banded metaphases showed a very rare cryptic insertion involving 22q11. While most genetic abnormalities in CML can be diagnosed using classical cytogenetics, molecular studies remain the gold standard in definitively identifying the characteristic BCR/ALB1 fusion. This case represents one of the variant cryptic rearrangements in CML where clinical correlation with morphologic, immunophenotypic, cytogenetics and FISH findings are indicated and highlights the importance of molecular testing at the time of primary diagnosis.