Detection of colorectal cancer at an early stage has been shown to significantly decrease mortality from the disease, while the advent of effective therapies for late-stage colorectal cancer make the detection of colorectal cancer at any stage a critical step in further reducing colorectal cancer mortality. Availability of a blood-based test for colorectal cancer is expected to improve screening compliance in the general population. Through DNA methylation-sensitive, restriction enzyme-based biomarker discovery, we identified a region of the Septin 9 gene that is methylated in over 90% of colorectal cancer tissues with little or no methylation seen in normal colon tissue and other controls. Specific detection of colorectal cancer DNA using the Septin 9 methylation biomarker ((m)SEPT9) was demonstrated in multiple studies of plasma from colorectal cancer patients and colonoscopy-verified negative controls. A prospective, population-based trial to determine the clinical performance of (m)SEPT9 in colorectal cancer screening guideline-eligible individuals has recently been completed, with the results to be published in the near future. The potential pitfalls and lessons learned in the multiyear process of developing the (m)SEPT9 biomarker from initial discovery to commercialization are described in this article.