Heart rate changes are related to many factors including gender. The autonomic changes accompanying emotion is the result of the activity of higher brain centres, which are responsible for analysing emotionally relevant stimuli. Studies examining the impact of changes in the level of female ovarian hormones on cardiac autonomic ragulation have produced inconsistent results. The purpose of the study was to determine whether there is a menstrual cycle effect on heart rate changes elicited by visual stimuli of different attractiveness. 12 healthy regularly cycling females (age 21-28 years) during the follicular phase and 12 females during the luteal phase have participated in the study. 90 pictures were selected from International Affective Pictures System (IAPS) including 30 neutral, 30 pleasant and 30 unpleasant pictures. Stimuli were presented by E-prime software and physiological data (heart rate) was collected using Biopac MP35 system. The duration of the experimental session was approximately 15 minutes. Salivary estradiol and progesterone levels were measured using an enzyme-linked immunosorbent assay (ELISA). Progesterone levels were found to be significantly higher in the luteal phase group (208.25 ±123.63 pg/mL) than in the follicular phase group (67.22 ±49.85 pg/mL), p<0.01. There were no significant differences in the salivary estradiol levels between the follicular and the luteal groups. Heart rate deceleration elicited by affective stimuli (duration 6s) comparing with the baseline period (1 minute before images presentation) was significantly stronger in the luteal phase group than in the follicular phase group, p=0.03. Different researchers have indicated that cardiac deceleration is the common response to unpleasant visual stimuli. Our results showed that heart rate deceleration was stronger in the luteal phase group than in the follicular phase group independently of the valence of pictures, although unpleasant pictures caused the largest changes.