BACKGROUND The aim was to examine the cost-effectiveness of magnetic resonance enterography (MRE) compared with computed tomography enterography (CTE) for routine imaging of small bowel Crohn's disease (CD) patients to reduce patients' life-time radiation-induced cancer risk. METHODS We developed a Markov model to compare the lifetime costs, benefits (measured in quality-adjusted life-years [QALYs] of survival and cancers averted) and cost-effectiveness of using MRE rather than CTE for routine disease monitoring in hypothetical cohorts of 100,000 20-year-old patients with CD. We assumed each CT radiation exposure conferred an incremental annual risk of developing cancer using the linear, no-threshold model. RESULTS In the base case of 16 mSv per CTE, we estimated that radiation from CTE resulted in 1,206 to 20,146 additional cancers depending on the frequency of patient monitoring. Compared to using CTE only, using MRE until age 30 and CTE thereafter resulted in incremental cost-effectiveness ratios (ICERs) between $37,538 and $41,031 per life-year (LY) gained and between $52,969 and $57,772 per quality-adjusted life-year (QALY) gained. Using MRE until age 50 resulted in ICERs between $58,022 and $62,648 per LY gained and between $84,250 and $90,982 per QALY gained. In a threshold analysis, any use of MRE had an ICER of greater than $100,000 per QALY gained when CT radiation doses are less than 6.0 mSv per CTE exam. CONCLUSIONS MRE is likely cost-effective compared to CTE in patients younger than age 50. Low-dose CTE may be an alternative cost-effective choice in the future.