Submicroscopic deletions of genes in recurrent chromosomal rearrangements occur frequently in hematologic malignancies, but their incidences have not been reported clearly. We investigated the incidence of submicroscopic deletions and their association with specific genetic rearrangements in various hematologic malignancies. A fluorescence in situ hybridization (FISH) study was conducted in 336 patients with acute lymphoblastic leukemia, 223 patients with acute myeloid leukemia, and 79 patients with chronic myelogenous leukemia. The incidence of submicroscopic deletions in patients with chromosomal rearrangements was the highest in the TEL/AML1 rearrangement (65.0%), followed by BCR/ABL (10.9%), MLL (5.6%), AML/ETO (4.0%), and PML/RARA (0.0%). Submicroscopic deletion was quite common, and incidences were variable according to disease entities and chromosomal translocations. To detect submicroscopic deletions, careful FISH study should be included for the cytogenetic study of hematologic malignancies, and their association with clinical prognosis needs to be further studied.