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Purpose. Squamous cell carcinoma (SCC) developing within fistulae and chronic wounds in patients with Crohn’s disease is a rare phenomenon with few reported studies in the literature. Clinical suspicion for SCC in Crohn’s disease patients with chronic painful fistulae is low, leading to delayed diagnosis and treatment. We present a patient with long-standing Crohn’s disease complicated by malignant degeneration of an enterocutaneous fistula tract. Methods. Workup with MRI, CT, and fistulogram revealed a 7 × 3 cm fistulous connection between a loop of small intestine and the patient’s perineum. Biopsies of the fistula tract confirmed the diagnosis of SCC. Results. The patient underwent an abdominoperineal resection with positive margins and is currently awaiting radiation therapy. Conclusions. This is the second case reported within the English literature of SCC arising from an enterocutaneous fistula in the setting of Crohn’s disease. Based on the findings in this case report and others presented in the literature, a high degree of suspicion of malignancy should be present in patients with chronic painful, poor-healing fistulae, especially in the absence of infection.