We performed this study to investigate the differences in radiological and laboratory findings between systemic juvenile idiopathic arthritis (s-JIA) and polyarthritis (p-JIA). Twenty-two patients with s-JIA and 18 with p-JIA were enrolled. Their laboratory findings and radiographs were examined retrospectively. Plain radiographs were obtained before the induction of biological agents. All radiographs were examined for the presence of soft tissue swelling, juxta-articular osteopenia, joint space narrowing, subchondral bone cyst, erosion, epiphyseal irregularity, and growth abnormalities. Carpal length and bone mineral density of the lumbar spine, an indicator of generalized osteoporosis, were also investigated in all the patients enrolled. Laboratory examinations involved white blood cell counts, platelets, C-reactive protein (CRP), rheumatoid factor (RF), anti-cyclic citrullinated peptide (CCP) antibody, and matrix metalloproteinase (MMP)-3. Comparisons of the laboratory findings between s-JIA and p-JIA indicated that the titers of anti-CCP antibody and RF were significantly increased in p-JIA sera (P < 0.05). There was no difference in BMD between the two groups of patients. Carpal length was significantly shorter in p-JIA patients than in s-JIA patients (P < 0.05). The most frequent radiological abnormality in s-JIA was juxta-articular osteopenia (93.8%), in comparison to a frequency of 50.0% in p-JIA. Joint space narrowing was shown in 9.8% of the s-JIA patients compared to 35.7% of the p-JIA patients. Subchondral bone cyst and erosion were more frequent in p-JIA than s-JIA. In conclusion, there were differences in radiographic characteristics and laboratory data between s-JIA and p-JIA in this study. In the radiological evaluation, bone-related abnormality was prominent in s-JIA and joint-related abnormality was striking in p-JIA, and these results indicated that the pathogenic bases of arthritis appear to differ between these two subtypes of JIA.