Background Ultrasonographic measurements of ovarian volume and antral follicle count are of clinical importance as diagnostic features of polycystic ovarian syndrome (PCOS), and as a parameter in estimation of ovarian follicular reserve in infertility care. Purpose To compare two-dimensional (2D)/three-dimensional (3D) transvaginal ultrasonography (TVUS) and magnetic resonance imaging (MRI) for estimation of ovarian volume and antral follicle count, and to assess reproducibility and inter-observer agreement of MRI measurements. Material and Methods Volumes of 172 ovaries in 99 women aged 21–37 years were calculated (length x width x height x 0.523) with conventional 2D TVUS and 2D MRI. Semi-automatic estimates of ovarian volumes were obtained by 3D MRI. Antral follicles were counted manually on 2D MRI and automatically by 3D TVUS (SonoAVC), and stratified according to follicle size. Results Mean ovarian volume assessed by 2D TVUS (13.1 ± 6.4 mL) was larger than assessed by 2D MRI (9.6 ± 4.1) and 3D MRI (11.4 ± 4.5) ( P < 0.001). Total follicle count was higher by 2D MRI than by 3D TVUS, mean difference 14.3 ± 16.2 follicles ( P < 0.001). In the smallest size interval of 1–3 mm the mean difference was 22.2 ± 17.6 ( P < 0.001). Intra- and inter-observer absolute agreement assessment for MRI measurements of ovarian volume and total follicle count showed ICC coefficients >0.77. Conclusion 2D MRI reveals more antral follicles, especially of small size, than 3D TVUS. Ovarian volume estimation by MRI provides smaller volumes than by the reference standard 2D TVUS. Ovarian volume estimation by 3D MRI, allowing independence of non-ellipsoid ovarian shape measurement errors, provides volumes closer to 2D TVUS values than does 2D MRI. Reproducibility and inter-observer agreement of 2D MRI measurements of ovarian volume and total follicle count are good.