Background and Aims: Bowel damage in Crohn's disease [CD] is defined as the presence of intestinal strictures, fistulas or abscesses. Early disease may represent a window of opportunity for timely intervention. We evaluated disease activity and severity by the Lemann Index [LI] and the Magnetic Resonance Index of Activity [MaRIA] score, and their prognostic value in early CD. Methods: All consecutive patients diagnosed with CD in two referral centres, assessed by magnetic resonance imaging or computerized tomography, were prospectively included. Disease activity and bowel damage in early CD, the correlation between the LI and the MaRIA score, and the value of cross-sectional imaging findings in predicting disease progression were assessed. Statistical analyses employed time-to-event methods. Results: We included 142 consecutive CD patients. Median time from diagnosis to baseline imaging was 0.3 years; median follow-up time was 4.9 years. At diagnosis, 39.4% of CD patients had bowel damage. At multivariable analysis, bowel damage and the LI were independent prognostic factors for intestinal surgery (hazards ratio [HR]: 3.21 and 1.11, respectively, p<0.001), and of CD-related hospitalization during patient follow-up [HR: 1.88, p=0.002, and 1.08, p<0.001, respectively]. Disease activity as expressed by the MaRIA score did not predict the disease course. The correlation between the LI and MaRIA score was weak [rho: +0.32; p<0.001]. Conclusion: Four out of ten CD patients have bowel damage at the time of the first imaging study. The presence of bowel damage, and not the MaRIA score, in early CD is associated with a worse outcome, with increased risks of surgery and hospitalization.