The aim of this study was to compare the radiological and clinical outcomes of early-onset scoliosis (EOS) patients with or without intraspinal anomalies (IAs) managed with growing rods (GRs), and to evaluate the safety of the GR technique in EOS patients with untreated IAs. EOS patients undergoing GR placement between August 2008 and July 2017 were retrospectively reviewed. Patients with untreated IAs were classified into the EOS+IA group, and those without IAs into the EOS-IA group. The radiographic parameters including Cobb angle of the major curve, T1-S1 height, and apical vertebral translation were measured, and a detailed assessment of the neurological status was performed at each visit. Seventy-six patients with EOS (32 boys, 44 girls) with an average age of 6.5 ± 2.3 years at initial surgery satisfied the inclusion and exclusion criteria, including 28 patients in the EOS+IA group and 48 patients in the EOS-IA group. The radiographic measurements were comparable between groups preoperatively, postoperatively, and at the latest follow-up. One patient in the EOS+IA group experienced sensory deficit in a unilateral lower extremity after initial surgery, and an intraoperative neurophysiological monitoring event was observed in a patient in the EOS-IA group. No permanent neurological deficit was observed in either group. EOS patients with and those without IAs had comparable clinical and radiological outcomes of the GR technique. Repeated lengthening procedures may be safe for EOS patients with untreated IAs.