Small bowel injury resulting from unforeseen penetration of the anterior annulus fibrosus and longitudinal ligament is a rare complication of lumbar microdiscectomy. The patient complained of abdominal tenderness and distention immediately after microdiscectomy for L4-5 and L5-S1 disc herniation. Using abdominal computed tomography, we found several foci of air overlying the anterior aspect of the vertebral body at the L5-S1 level. Segmental resection of the small bowel including small tears and primary anastomosis of the jejunum were performed. Here, we present a case of intestinal perforation after lumbar microdiscectomy and discuss technical methods to prevent this complication with a review of literature.