Changes in the DNA methylation profile, including general genomic hypomethylation and regional hypermethylation, have been shown to coexist in many neoplastic tissues. However, the relationship between, and significance of, these different forms of DNA methylation dysregulation in disease onset, progression, or maintenance remains unclear. Previously, our work has shown that the CpG dinucleotide-rich gene Myf-3 is hypermethylated in most cases of malignant lymphoproliferative disease (LPD). However, it is unknown whether malignant transformation of lymphoid cells is associated with general genomic hypomethylation and whether regional hypermethylation is restricted to CpG islands. The relationship between the status of general genomic methylation and the methylation of CpG and non-CpG islands can be clearly investigated in DNA from tumors of patients suffering malignant LPD, as monoclonalilty of malignant cells in LPD can be readily confirmed. In this study, the relationships between the methylation status of a region of the PAX7 paired box, which is not contained within a CpG island, general genomic hypomethylation, and the methylation status of Myf-3 was examined in 24 cases of LPD. Results revealed that hypermethylation of the PAX7 paired box is strongly associated with hypermethylation of Mvf-3, indicating the abnormal hypermethylating activity in malignant lymphoid cells does not specifically target CpG islands. Further, general genomic hypomethylation was shown to be associated with malignant LPD but not with regional hypermethylation, indicating that the mechanisms responsible for the generation of each of these disturbed DNA methylation phenotypes act independently as one of a number of permissive but not essential steps in the malignant transformation of lymphoid cells.