Background information on how biological factors influence the level of bone turnover markers is crucial in order to make proper use of these measurements. In the present study, which is part of the fourth survey of a general population in Tromsø, Norway, we evaluated the variation in the bone formation markers bone alkaline phosphatase (S-BAP) and osteocalcin (S-OC) in 528 men and 605 women, age 25–74 years. In the Tromsø Study in 1994/5, the whole population above 25 years was initially invited and 7948 individuals attended an extended examination (76.4% of the invited population). The present study population is a random sample of these attendees. The variation with age, gender, height, weight, body mass index and season, and with menopausal status in women, was examined. In men there was a decrease in S-OC up to the age of 56 years with little further change, while S-BAP showed no change with age. Among women, variation in bone markers was mainly observed to change with menopause, with a 41% and 21% increase in the mean level of S-BAP and S-OC, respectively. There was a negative trend in S-OC with body mass index in both men and women. A seasonal change of 20% in the level of both bone markers in men and of S-BAP in postmenopausal women was observed in this region at a far northern latitude. We conclude that, of the factors examined, season and menopausal status must be taken into account when measuring these bone formation markers.