We investigated the short-term (1 hour-3 days) effects of a 45 minute run on calcium, parathyroid hormone, the carboxyterminal propeptide of type I procollagen (PICP), and the immunoactive carboxyterminal telopeptide of type I collagen in serum (ICTP) in young females. Fourteen healthy young women, aged 25.2 ± 0.6 years (mean ± SEM) with regular menstruations, participated. The test was outdoor jogging for 45 minutes at an intensity of 50% of VO2 max. Blood samples were collected 15 minutes before the test and 1, 24, and 72 hours after the test. The measured values were adjusted for changes in plasma volume. A significant decrease of ionized calcium was observed at 1 hour (P < 0.001) and 72 hours (P < 0.05) and a significant increase of parathyroid hormone (PTH) was noted 24 (P < 0.01) and 72 hours (P < 0.05) after the test. A significant decrease of PICP at 1 hour (P < 0.05) was followed by an increase after 24 (P < 0.01) and 72 hours (P < 0.001) and a significant increase in ICTP was noted at 24 and 72 hours (P < 0.05). A strong positive correlation was found between serum levels of PICP and ICTP (r = 0.55–0.84; P < 0.05) throughout the experiment. In conclusion, young females showed biochemical signs of increased bone collagen turnover and altered homeostasis of calcium and PTH after a single bout of moderate endurance exercise.