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Introduction: Colorectal Cancer (CRC) is a common type of cancer with a rising prevalence worldwide. Morbidity and mortality of CRC can be reduced by screening programs and early diagnosis. Currently used screening tests include fecalbased methods are non-invasive and inexpensive, however the sensitivity and specificity of these tests are not high enough. Aim: To evaluat hypermethylation of Bone Morphogenic Protein 3 (BMP3) as a biomarker in early diagnosis of CRC. Materials and Methods: A total of 96 individuals were enrolled in the present case-control study (59 CRC patients versus 37 healthy controls) and Methylation-Specific Polymerase Chain Reaction (PCR) was used to evaluate methylation status of the BMP3 gene in plasma samples and colonoscopy tissue biopsies. Results: In plasma samples, 75% of CRC patients showed hypermethylation in the BMP3 gene versus only 30% of the controls. In colonoscopy tissue biopsies, BMP3 showed hypermethylation in 81.6% of CRC patients. Specificity and sensitivity of this gene in CRC diagnosis were found to be 76% and 66% respectively. Conclusion: The results of the present study showed that BMP3 in combination with other genes could be used as a noninvasive and promising biomarker in screening and diagnosis of CRC.