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Sacroiliac (SI) joint dysfunction is a significant contributor to low back pain. Percutaneous SI joint fusion is a minimally invasive procedure that can provide excellent pain relief for patients, but it is not without complications, especially in patients with abnormal lumbosacral anatomy. We report the case of a 71-year-old man with sacral dysmorphism who had a painful SI joint that was refractory to conservative therapy. After undergoing an elective percutaneous SI joint fusion, he was discharged in stable condition. He returned in a delayed fashion with a large subgluteal hematoma. Imaging revealed disruption of a branch of the superior gluteal artery (SGA). Surgical exploration and ligation of the SGA were undertaken. Sacral dysmorphism affects SI joint fusion procedures by altering sacral anatomy and the safe zones for SI joint implants. Variations in lumbosacral anatomy can also alter the course of the SGA and adjacent nerves. Due to the wide prevalence of sacral dysmorphism, especially in the setting of low back pain, pre-surgical planning to avoid iatrogenic injuries must be considered with advanced imaging studies such as a computed tomography angiogram of the pelvis or catheter-based angiogram, or alternative surgical approaches to the SI joint must be taken.