Aim: To summarize current approaches to diagnosing and evaluating clinical features and disease course of Crohn’s disease, and to provide competency-based practical recommendations for diagnostic assessment in children with early-onset disease. Materials and Methods: Literature analysis was conducted using electronic databases (PubMed, Medline, the Cochrane Library) and the author’s clinical cases of Crohn’s disease in 7 children aged 1 year 10 months to 4.5 years. The diagnostic algorithm in young children included general clinical examination and laboratory and instrumental methods, including genetic testing and serological markers. Morphological verification of the diagnosis by histological examination of biopsy specimens is mandatory. Conclusions: Delayed diagnosis of Crohn’s disease in young children results from nonspecific symptoms, variable early manifestations, and prominent extraintestinal features. Early-onset disease poses a major diagnostic challenge and requires increased awareness of extraintestinal manifestations, perianal lesions, and growth failure. Serological tests serve as supportive tools and do not exclude the diagnosis when negative, particularly in children under 6 years. Genetic screening to rule out primary immunodeficiencies is an essential part of the diagnostic workup in this age group.