Background Polycystic ovary syndrome (PCOS) is associated with frequent overweight and abdominal obesity. Quantifying visceral adipose tissue (VAT) in PCOS patients can be a tool to assess metabolic risk and monitor effects of treatment. The latest dual-energy X-ray absorptiometry (DXA) technology can measure VAT and subcutaneous adipose tissue (SAT) in a clinical setting. Purpose To compare DXA-measurements of VAT and SAT with the gold standard MRI in women with PCOS. Material and Methods A cross-sectional study of 67 overweight women with PCOS was performed. Measurements of VAT and SAT were performed by DXA in a 5-cm thick transverse slice at the L4/L5 level and by MRI in a 1-cm thick transverse slice at the L3 level. Results Mean (SD) DXA-VAT was 81 (34) cm3, DXA-SAT was 498 (118) cm3, MRI-VAT was 117 (48) cm3, and MRI-SAT was 408 (122) cm3. MRI and DXA measures of VAT (r = 0.82, P < 0.001) and SAT (r = 0.92, P < 0.001) correlated closely, and DXA-VAT was stronger correlated with MRI-VAT than BMI (r = 0.62, P < 0.001) and waist circumference (r = 0.60, P < 0.001). DXA-VAT coefficient of variance was 6.7% and inter correlation coefficient was 0.98. Bland-Altman analyses showed DXA to slightly underestimate VAT and SAT measurements compared with MRI. Conclusion DXA and MRI measurements of VAT and SAT correlated closely despite different size of region of interest, and DXA-VAT was superior to waist circumference and BMI in estimating MRI-VAT. DXA showed high reproducibility making it is suitable for repeated measurements in the same individual over time.