Widespread hypomethylation of DNA and regional hypermethylation, including tumor suppressor regions, have been demonstrated in several human cancers. Since a highly heterogeneous array of genetic anomalies have been associated with breast cancer, we examined several chromosomal hot spots for abnormal methylation patterns. Low-levels of increased methylation of HRAS (11p15) were observed between normal and tumor breast tissue samples from 8 patients. No noticeable variation in methylation was observed with DNA probes from chromosomes 11p15, 1p36, 17q22, 17p13.3 and 3p21 for the 7 ductal breast carcinoma patients, though some variability was observed for a patient with atypical medullary carcinoma. Additionally, the methylation pattern of the estrogen-receptor gene (6q24-27), whose protein product is increased in numerous breast cancers, also did not change. Therefore, as opposed to other cancer types, widespread hypomethylation and regional hypermethylation do not appear to be involved in the early stages of breast cancer and does not account for the molecular heterogeneity of the disease. Proposed alternative mechanisms for the diversity of genetic alterations associated with breast cancer are discussed.