Human tumor suppressor gene beclin 1 regulates cell growth through autophagy. The mRNA expression of beclin 1 was reported to be down-regulated in breast cancer with high frequency of loss of heterozygosity (LOH). However, there was no report about the expression levels or the regulatory mechanisms of beclin 1 in gastric and colorectal cancer. Both the mRNA and protein expression levels of beclin 1 was detected in the tissues of gastric and colorectal cancers, as well as the aberrant DNA methylation and LOH related to the expression of beclin 1. By comparing with normal tissues adjacent to the tissue of these tumors, it was found that beclin 1 mRNA expression levels were significantly decreased in gastric tumor tissue. Furtherly by explorating the 5′ region of beclin 1 gene sequence, a large and dense CpG island was discovered and meanwhile methylations in the promoter and the intron 2 regions of beclin 1 were found in both gastric and colorectal tumors. And LOH was found in gastric tumors. These findings suggested that aberrant DNA methylation, as well as LOH, were involved in the regulation of beclin 1 expression in gastric and colorectal cancer.