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This case report details the diagnostic and therapeutic approach of a young male presenting with an ileal nodular lesion of uncertain aetiology whose final diagnosis was gastric heterotopia within a Meckel’s diverticulum. The case underscores the challenges of diagnosing ileal lesions due to the overlapping of clinical presentations of benign and malignant conditions. It highlights the importance of integrating advanced diagnostic tools and a multidisciplinary team approach to ensure accurate diagnosis and effective treatment.