Hormones are of crucial importance for human behavior. Cyclical changes of ovarian hormones throughout women's menstrual cycle are suggested to underlie fluctuation in masculinity preference for both faces and bodies. In this study we tested this hypothesis based on daily measurements of estradiol and progesterone throughout menstrual cycle, and multiple measurements of women's preference towards masculinity of faces and bodies of men. We expected that due to a large variation among daily hormonal levels we would not observe a direct effect of daily hormone levels, but rather that average levels of ovarian hormones throughout the cycle (a reliable marker of a probability of conception) would better predict women's preferences. We found a negative relationship between average progesterone levels and facial masculinity preference, but only among women who were in long-term relationships. There was no relationship between facial masculinity preference and either of the estradiol or progesterone daily levels. Similarly, only average levels of hormones were significantly related to facial symmetry preference. For women who were in relationships estradiol was positively related to symmetry preference, while for single women this relationship was opposite. For body masculinity preference there were no significant relationships with neither averaged nor daily hormonal levels. Taken together, our results further suggest that overall cycle levels of ovarian hormones (averaged for a cycle) are better predictors of facial masculinity and symmetry preference than daily levels assessed during preferences' tests. Importantly, including information about relationship status in the investigations of hormonal bases of preferences is crucial.