Recently, gene expression studies suggested an alternative model in which the ability to metastasize is an early event that can already be distinguished even in primary tumors. Altered expression of multiple genes and micro RNAs have been implicated in this process, but the GANT61 Hedgehog inhibitor molecular mechanisms underlying these alterations are unknown. Recent reports have also shown that DNA methylation has prognostic implications in CRCs. Patients with CRCs that are microsatellite stable and have CpG islands methylator phenotype tend to have a worse prognosis when compared with other molecular subtypes of CRCs. Promoter DNA methylation and associated silencing is a frequent and early event in colorectal carcinogenesis. Some of the genes affected, such as MLH1, p16 and p14, clearly contribute physiologically to the neoplastic phenotype. The occurrence of liver metastasis leads to a poor clinical outcome in CRCs, and here we sought to determine the possible involvement of DNA methylation in the process. Generally, we found that methylation does not increase with increasing stage, confirming that it is an early event. Importantly, we did find substantial drift in methylation patterns in liver metastases compared to primary tumors, but the patterns at loci examined appeared more consistent with random flux rather than selection for specific genes. When we looked at the differences in methylation between primary tumors with and without liver metastases, methylation levels of p14, TIMP3 and HPP1 progressively decreased from early-stage to late-stage disease. We have previously found that methylation of p14 and TIMP3 is the markers for predicting CIMP1. Thus, this consistent decrease of methylation in CRCs with liver metastasis likely represents the generally good prognosis of CIMP1 cancers which rarely progress to advanced disease. Depletion of TIMPs has been reported to abrogate normal apoptotic programs, enhance primary tumor growth and angiogenesis, invasiveness, and metastasis and possibly contribute to all stages of malignant progression including metastasis. Our data are not consistent with a major role for TIMP3 in CRC metastasis. It is possible that other members of the TIMP family such as TIMP1 and TIMP2 might be more important for the liver metastatic process in CRCs. Overall, we quantitatively compared the methylation status of 21 genes between paired primary and liver metastasis lesions. Of these, only MGMT methylation was consistently higher in the liver metastases than primary tumors. Of 16 pairs studied, five showed significantly higher MGMT methylation at the metastatic site. Of these five tumor pairs, four pairs demonstrated MGMT methylation at both sites with an increase in methylation density. Increased density of methylation could be explained by multiple different factors – increased proportion of methylated cells, switch from monoallelic to biallelic methylation or even differences in the degree of normal cell contamination of the tumor samples.