Aim of this study is to measure the volume of the uterine layers in healthy women according to the menstrual cycle phases and to test the agreement between three methods. The study was performed with 28 healthy women. Participants were divided into three groups as follicular (n=7), luteal (n= 10) and postmenopausal phase (n= 11). We used the point-counting and planimetry method in MR images and the ellipsoid methods in images obtained by transvaginal ultrasonography. Spearman correlation analysis showed significant negative correlations between the volumes of uterine layers and age (p<0.01). The volumes of the total uterus, the total myometrium and the endometrium measured with planimetry and point-counting methods were significantly lower in the postmenopausal women (p<0.01). While volumes of total uterus and the total myometrium significantly lower in the postmenopausal group in measurements done using ellipsoid method, the decrease in the volume of the endometrium was not statistically significant. The Bland-Altman test results indicated an excellent agreement between point-counting and planimetry methods in the volumetric measurements. The ellipsoid method might be inadequate for determining uterine layers volume particularly the endometrium volume. The stereological methods permit unbiased and efficient estimation of volume of uterine layers in vivo examination of MRI.