Introduction: Heterochromatin consists of DNA sequences that are not transcribed, and are repeated in short tandem at heterochromatic regions of chromosomes 1, 9, 16 as well as the distal part of long arm of chromosome Y. Slightly large tandem repeats at the centromeres of human chromosomes are also considered as heterochromatin regions. The main aim of the present study is to evaluate the heterochromatin polymorphism associated with chronic myeloid and acute non-lymphocytic leukemias. Material and Methods: 16 Leukemic patients and 10 normal healthy persons were selected. By applying Barium Hydroxide Saline Giemsa (BSG) method. The variant heterochromatin of chromosome 1, 9 and 16 on bone marrow samples and lymphocyte cultures were evaluated. Results: the result of present study indicated no significant differences for heteromorphisms between Acute Non-Lymphocytic Leukemia (ANLL) Patients and normal individuals. But differences were significant on comparing the complete inversions in ANLL patients with the controls. There were significant differences in heterochromatin variant of C-segment in chromosomes 1 and 9 between Chronic Myeloid Leukemia patients (CML) and normal group. Partial and complete inversion between CML patients and the control group is significant. Conclusion: A number of reports have indicated pronounced heteromorphism in size and localization in constitutive band region of chromosomes 1, 9 and 16 in many malignancies. However, this study showed similarities and dissimilarities with other investigators regarding heterochromatin variations and inversions.