To evaluate ovarian morphology using three-dimensional magnetic resonance imaging (MRI) in adolescent girls with and without polycystic ovary syndrome (PCOS). Also compare the utility of MRI versus ultrasonography (US) for diagnosis of PCOS. Cross-sectional study. Urban academic tertiary-care children's hospital. Thirty-nine adolescent girls with untreated PCOS and 22 age/body mass index (BMI)-matched controls. Magnetic resonance imaging and/or transvaginal/transabdominal US. Ovarian volume (OV); follicle number per section (FNPS); correlation between OV on MRI and US; proportion of subjects with features of polycystic ovaries (PCOs) on MRI and US. Magnetic resonance imaging demonstrated larger OV and higher FNPS in subjects with PCOS compared with controls. Within the PCOS group, median OV was 11.9 (7.7) cm(3) by MRI compared with 8.8 (7.8) cm(3) by US. Correlation coefficient between OV by MRI and US was 0.701. Due to poor resolution, FNPS could not be determined by US or compared with MRI. The receiver operating characteristic curve analysis for MRI demonstrated that increasing volume cutoffs for PCOs from 10-14 cm(3) increased specificity from 77%-95%. For FNPS on MRI, specificity increased from 82%-98% by increasing cutoffs from ≥ 12 to ≥ 17. Using Rotterdam cutoffs, 91% of subjects with PCOS met PCO criteria on MRI, whereas only 52% met criteria by US. Ultrasonography measures smaller OV than MRI, cannot accurately detect follicle number, and is a poor imaging modality for characterizing PCOs in adolescents with suspected PCOS. For adolescents in whom diagnosis of PCOS remains uncertain after clinical and laboratory evaluation, MRI should be considered as a diagnostic imaging modality.