The objective of the study was to determine the extent to which the FLU-FOBT Program, a colorectal cancer screening (CRCS) intervention linking the provision of fecal occult blood tests (FOBT) to the time of annual influenza vaccination, resulted in practice changes in six primary care clinics 1 year after it was introduced in a randomized controlled trial (RCT). We assessed CRCS rate changes for influenza vaccine recipients, administered brief serial clinic staff surveys and interviewed clinic leaders 1 year after the RCT. CRCS rates for influenza vaccination recipients between the ages of 50 and 75 years were 42.5% before the RCT, 54.5% immediately after the RCT and 55.8% 1 year after the RCT (P < 0.001 for difference between baseline and 1 year after RCT). Many FLU-FOBT Program components were maintained in most clinics at 1-year follow-up. Only 63% of clinic staff survey respondents (26 of 41) continued offering FOBT with influenza vaccines, but 85% (35 of 41) continued to provide mailing kits with FOBT. Many patient education materials were maintained and staff satisfaction with the intervention remained high. Clinic leaders acknowledged barriers to maintenance but also observed several beneficial practice changes. Many components of the FLU-FOBT Program were maintained, with beneficial outcomes for participating practices.