Stricturing or penetrating lesions develop over time in most patients with Crohn's disease. The Lémann Index indicates the degree of digestive damage at a given time in 1 individual. We tracked changes in Lémann Index scores in an inception cohort of patients and looked for factors associated with digestive damage. We studied 221 patients diagnosed with Crohn's disease from 2004 through 2011 who received 2 or 3 serial morphological evaluations over a period of 2-10 y. We collected cross-sectional images and had them reviewed by a gastroenterologist and a radiologist; Lémann index scores were calculated. A value of 2 was chosen as the cut-off for substantial transparietal damage. Factors associated with score >2 at last evaluation and progression of index scores were identified using univariate analysis and logistic regression analyses. Median index Lémann Index scores were 2.3 (intra-quartile range [IQR], 1.2-3.9) at first evaluation, 3.5 (IQR, 1.2-8.6) 2-5 y after diagnosis, and 8.3 (IQR, 1.2-12.1) 5-10 y after diagnosis. Index scores increased significantly at each stage compared with initial or previous values (P<.0001). After 73 months (IQR, 51-96) of follow up, 138 patients had a Lémann Index score >2.0. The only early factor that predicted later damage was first index value. Intestinal resection, time, and percentage of time elapsed with a clinically active disease were associated with progressing damage. Based on an analysis of patients with Crohn's disease using the Lémann Index, nearly two thirds have substantial mucosal damage 2-10 y after diagnosis. High Lémann index scores at first evaluation, time, persistent clinical activity, and intestinal resection are associated with damage.