We present a case of a 17-year-old so far healthy and normally developing boy, who was admitted to our Department due to perianal fistulas persisting for three years. Previous diagnostic procedures, including colonoscopy, failed to provide the diagnosis. No improvement was observed after repeated surgical interventions and oral antibiotic therapy. A suspicion of Crohn’s disease was raised. Full diagnosis was performed: gastroscopy and colonoscopy with biopsy, magnetic resonance enterography, and pelvic magnetic resonance. Crohn’s disease was diagnosed based on the overall clinical picture and laboratory findings. The aim of this paper was to emphasise the importance of early targeted diagnosis to avoid diagnostic delay and thus reduce the risk of complications. A general practitioner, who provides primary care and refers his patients for additional tests and consultations, plays a very important role in this process. Therefore, by describing the case of this young patient, we aimed to draw attention to some typical symptoms that may be the very first manifestations of chronic inflammatory bowel disease. The chronic or recurrent perianal lesions in an otherwise normally developing adolescent showing no other gastrointestinal symptoms should be a motivation for performing full diagnosis for Crohn’s disease.