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The most commonly used noninvasive test for colorectal cancer (CRC) screening has been the guaiac fecal occult blood test (gFOBT). The fecal immunochemical test (FIT) detects CRC and colorectal polyps with higher levels of sensitivity than the gFOBT, and may be more acceptable to patients. However, the FIT has not replaced the gFOBT in many clinical settings. We analyzed data from a large healthcare system that replaced the gFOBT with the FIT to determine the effects on CRC screening.We conducted a retrospective observational study of 7898 patients at the Veterans’ Administration San Diego Healthcare System, 50–75 years old, who were offered stool-based CRC screening as part of primary care March 2014 through January 2015. Test orders and results were extracted from electronic health records; we performed manual reviews of colonoscopy and pathology reports for Veterans with positive results from the tests. Our primary outcome was test completion within 1 year of order; secondary outcomes were positive results and detection of advanced neoplasia by diagnostic colonoscopy. The primary analysis used an intention-to-screen approach, which included all patients with test orders; as-screened analyses were also performed.Among 7898 patients, 3236 had gFOBT and 4662 FIT orders. In the intention to screen analysis, a significantly higher proportion of subjects completed a FIT (42.6%) than a gFOBT (33.4%) (P < .001); advanced neoplasia was detected in a significantly higher proportion of subjects offered a FIT (0.79%) than a gFOBT (0.28%) (P = .003). The numbers needed to invite to achieve 1 additional completed test and identify 1 additional patient with advanced neoplasia were 11 and 196, respectively.In a retrospective study of patients at a Veterans’ administration healthcare system, replacing the gFOBT with the FIT increased the proportion of patients who completed CRC screening. Replacement of the gFOBT with the FIT should be strongly considered by all healthcare systems.