BACKGROUNDS: The disease course of inflammatory bowel disease (IBD) is highly variable; early and precise identification of patients with poor outcomes is crucial. We aimed to classify the long-term disease course of IBD using biochemical markers and evaluate the clinical factors associated with different disease courses. METHODS: A latent class mixed model was employed to identify distinct trajectories of C-reactive protein (CRP) and fecal calprotectin (FCP) levels in 256 and 635 patients with Crohn's disease (CD) and ulcerative colitis (UC), respectively, from a tertiary hospital cohort. Multinomial logistic regression was used to evaluate the relationships between various trajectories and clinical variables. RESULTS: Three trajectories were identified for CD and UC: class 1, early and sustained biochemical remission; class 2, delayed remission; and class 3, prolonged difficulty in achieving remission for > 5 years. For patients with CD, early immunomodulator initiation was associated with a high likelihood of belonging to class 1 in the CRP trajectory analysis, whereas early advanced therapy increased the probability of belonging to class 1 in the FCP trajectory analysis. CRP trajectory analysis showed no significant associations in patients with UC. Younger age at diagnosis and early immunomodulator initiation were associated with higher odds of being in class 2 or 3, whereas current smoking was associated with a high likelihood of being in class 1 in the FCP trajectory analysis. CONCLUSIONS: Early aggressive medical treatment for CD may lead to long-term biochemical remission, whereas no similar association was observed in UC.