Background: Multiple external root resorption (MERR) has been reported in systemic sclerosis (SSc) patients in Japan and Spain. To establish whether MERR is a new manifestation, we investigated the prevalence of MERR and systemic and oral manifestations to be associated with MERR in patients with SSc. Methods: Root resorption was detected by dental X-rays, panoramagraphy or cone beam computed tomography (CBCT). The prevalence of systemic and oral manifestations was examined by rheumatologists and dentists, respectively. Autoantibodies were investigated using laboratory tests. Results: MERR was detected in four out of the 41 patients (9.8%) who participated in the present study. The prevalence of digital ulcers was significantly higher in patients with MERR (MERR vs. non-MERR, 75% vs. 16.2%, p < 0.05), whereas that of other systemic manifestations was not. The prevalence of face skin sclerosis (100% vs. 10.8%, p < 0.01), calcinosis at the facial region (75% vs. 0%, p < 0.01), limited mouth opening (75% vs. 18.9% p < 0.05), temporomandibular disorder symptoms (50% vs. 2.7%, p < 0.05), and tongue rigidity (75% vs. 2.7%, p < 0.05) was significantly higher in patients with MERR. Conclusion: SSc patients with MERR had highly homogenous maxillofacial manifestations. Further clinical and basic studies are needed to elucidate the mechanisms underlying MERR in SSc patients.