Background Changes in oestradiol and progesterone hormones and associated fluid retention during the menstrual cycle phases might affect body composition (BC) in women. Aim The main objectives of this study were to determine the changes in whole and segmental BC by dual-energy x-ray absorptiometry (DXA) and bioelectrical impedance (BIA) during the mid-follicular (MFP) and mid-luteal (MLP) phases. Subjects and methods Thirty recreationally active young women participated in this study. BC was measured by DXA and BIA during MFP and MLP. A mixed linear model for repeated measures analysis was used to determine the differences between the two phases. Results Body mass was higher during MLP than MFP, while total body water, total and segmental fat mass and fat percentages measured by both BIA and DXA were similar during the two phases. DXA-derived fat-free mass and soft lean mass in the android region were higher during MLP than MFP. Large variability in individual responses was evident. Conclusion On average, whole and segmental BC variables do not change significantly between MFP and MLP. However, given the large variability among the individual responses, it is suggested to perform repeated BC measurements during the same phase of the menstrual cycle.