The purpose was to investigate changes in neuropeptide Y (NPY) protein and dipeptidyl peptidase IV (DPP-IV) activity in the plasma and saliva in normally cycling women and women after menopause. We recruited 7 cycling women and 7 postmenopausal women for a cross-sectional, prospective pilot study. Blood via venipuncture and saliva samples were taken at each point in the menstrual cycle (premenopausal) or once per week (postmenopausal) for 2 months. Blood and saliva were analyzed for estrogen, NPY using ELISA and DPP-IV activity using a fluorometric assay. Plasma β-estradiol was an average of 96.45 ± 57.04 pg/mL over 2 cycles in the premenopausal group and 1.72 ± 0.35 pg/mL over 2 months in the postmenopausal group (P < .05). In the cycling group, there were no significant differences in saliva or plasma NPY or DPP-IV over the cycle. For the postmenopausal group, salivary NPY and DPP-IV did not change over 2 months. Plasma NPY was lowest in the middle 2 weeks (average: 0.52 ± 0.10 ng/mL) compared to the first and fourth weeks (average of week 1 and 4: 0.60 ± 0.14 ng/mL; P < .05). Plasma NPY in postmenopausal women was higher overall (0.56 ± 0.13 ng/mL) compared to cycling women (0.30 ± 0.11 ng/mL; P < .05). Plasma DPP-IV activity was unchanged by time in the postmenopausal group. Saliva DPP-IV and saliva NPY in the cycling group had a significant negative correlation (R = -0.95; P < .05). We found that saliva measures of NPY and DPP-IV activity appear to be poor estimates of plasma concentrations and activities, but a larger sample size is required to conform this. Differences in plasma NPY concentrations between the groups and the relationship between salivary NPY and DPP-IV suggests that there may be some unique differences between these groups.