Objective To evaluate the diagnostic accuracy of the aberrant methylation of genes in stool for colorectal tumor. Methods Databases including The Cochrane Library, PubMed, EMbase, CBM, Web of Science, CNKI and WanFang Data were searched to collect the diagnostic trials on the aberrant methylation of genes in stool for colorectal tumor published from January 1990 to February 2012. QUADAS items were used to evaluate the quality of the included studies, and the meta-analysis was conducted using Meta-Disc 1.4 software. Results A total of 32 studies involving 3 951 patients were included. The results of meta-analysis showed that, for detecting the colorectal tumor, the weighted sensitivity, specificity, diagnostic odds ratio (DOR), area under the summary receiver operating characteristic (SROC) curve and Q were 92% (95%CI 91% to 93%), 63% (95%CI 61% to 65%), 20.79 (95%CI 15.13 to 28.57), 0.861 9 (SE=0.020 4), and 0.792 6 (SE=0.019 8), respectively. For detecting the colorectal cancer, the weighted sensitivity, specificity and area under the curve (AUC) were 91% (95%CI 89% to 92%), 75% (95%CI 73% to 77%), and 0.900 7, respectively. For detecting the colorectal adenoma, the weighted sensitivity, specificity and AUC were 79% (95%CI 76% to 83%), 75% (95%CI 73% to 77%), and 0.845 7, respectively. Conclusion With high sensitivity (92%) and moderate specificity (63%), aberrant methylation of genes in stool can be used as an optional noninvasive method for the diagnosis of colorectal tumor.