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Abstract Background Angiomyolipoma with epithelial cysts is a rare variant of an angiomyolipoma that typically occurs sporadically. Patients with pre-existing kidney lesion or disease have significantly increased risk of morbidity and mortality associated with trauma. Abnormal and diseased kidneys are frequently injured by low or insignificant velocity impacts. The vulnerability of these kidneys is related to the type of pathology. However, cystic or hydronephrotic kidneys are more susceptible to trauma. Recent studies have shown an association of this rare entity with tuberous sclerosis complex. Despite the rarity of genetic association of Angiomyolipoma with epithelial cysts and tuberous sclerosis, the emerging findings raise the necessity of genetic testing of these lesions to confirm a remote possibility of tuberous sclerosis complex. Case presentation We report a case of a 38-year-old male patient who sustained a right renal injury as a result of a gunshot to the abdomen and underwent an emergency nephrectomy due to hemodynamic instability. A grossly looking shattered kidney was surgically removed. The morphology in conjunction with immunohistochemistry of the specimen favoured a diagnosis of Angiomyolipoma with epithelial cysts. Conclusion This is the first reported case of angiomyolipoma with epithelial cysts diagnosed on a nephrectomy specimen from renal trauma. We aim to highlight an approach to renal trauma on a kidney with pre-existing AMLEC as well as an approach to adult cystic renal neoplasms and to propose the importance of genetic testing for Tuberous Sclerosis.