Menstrual symptoms include some rhythmical changes and stress perception but women differ in duration and severity of these symptoms. It is not known whether these differences are associated with cortisol awakening response (CAR). The aim of the current study was to follow young women daily for the CAR and menstrual parameters throughout the whole menstrual cycle. Healthy and regularly cycling young women (n = 16, 17 to 31-year-old) participated in the current study. The daily records of severity of problems (DRSP) was filled in daily by the participants. CAR was also assessed daily form the salivary samples collected at a 0-, 15-, 30- and 60-min post-awakening. In terms of daily awakening cortisol profiles, women had either 2-20 (n = 3), or 20-200 (n = 8) or 200-2000 (n = 5) ng/ml cortisol according to the median levels throughout their cycle. CAR was weakly and negatively correlated with DRSP scores but strongly and positively with oestradiol (R-2 = 0.300; p = 0.000) and progesterone (R-2 = 0.490; p = 0.000) concentrations. Individuals with higher oestradiol and progesterone concentrations did not have high DRSP scores. In conclusion, CAR had a very high between-subject difference but had a low within-subject difference throughout the days of menstrual cycle, suggesting that CAR is a relatively stable personal trait. Moreover, the interplay between cortisol, progesterone and oestradiol appears to be important for the severity of menstrual symptoms.