BS69 was originally identified as an adenovirus E1A-binding protein and was found to be involved in multiple cellular events. A recent array-based study implicated the presence of copy number variations (CNVs) of BS69 in the genomes of acute myelogenous leukemia. CNVs are present in the general population at varying degrees and have been found to associate with various types of diseases including hematological malignancies. However, most of the current studies focused on the genome-wide screening of CNVs, and the functional impact of such regions needs to be extensively investigated in large amount of clinical samples. Thus, in our study, we collected 617 bone marrow samples from multi-types of hematological malignancies as well as healthy controls. We found significant association between the CNVs of BS69 and these hematological malignancies including acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), multiple myeloma (MM), and myelodysplastic syndrome (MDS). We also examined the expression of BS69 mRNA in the samples with one or two copies of DNA, and observed a weak yet positive correlation between the relative expression level and gene dosage. In general, the CNVs of BS69 have the potential to serve as a diagnostic indicator, alone or in combination with other markers, for hematological malignancies.