The aim of this study was to evaluate risk factors associated with the relapse rate in the first year and the need for surgery in children with Crohn's disease (CD). Data of all children (n = 74) diagnosed with CD from January 2004 to June 2011 were retrospectively analyzed. Multivariate Cox proportional hazards regression model was used to assess whether important clinical variables at diagnosis (age, presence of perianal disease, first induction therapy, first maintenance therapy, levels of Pediatric CD Activity Index (PCDAI), C-reactive protein (CRP), and standard deviation score (SDS) for height for weight) were associated with the risk of clinical recurrence in the first year and need for surgery during follow-up. Relapse occurred in 36 (48.6%) patients in the first year from diagnosis. The only significant parameter associated with negative risk of relapse in the first year was exclusive enteral nutrition (EEN) used as induction therapy (hazard ratio (HR) 0.469, 95% confidence interval (CI) 0.232-0.948). EEN induced remission in 84.2% of patients. The only risk associated with EEN treatment failure was the involvement of the upper gastrointestinal tract. During the follow-up, 25 (33.7%) patients underwent surgery. The multivariate Cox regression model failed to recognize significant risk factor for surgery. This study underlines the importance of early EEN in the treatment of CD; it is not only efficacious in the remission induction but could also prevent relapse in the first year.