During growth, bones change their dimensions rapidly with the changes involving both formation and resorption processes. Small cross-linked peptides coming from type I collagen molecules are excreted in urine when bone is resorbed. To date, conflicting results have been presented concerning the age- and puberty-related changes of urinary markers. The purpose of the present study was to verify the effect of age, gender, and puberty on the urinary excretion of type I collagen degradation products in healthy children and adolescents. Timed spot urines from 176 children (4–20 years old) and 50 young adults were analyzed. The concentrations of N-telopeptides of type I collagen (NTx), pyridinolines (Pyr), and deoxypyridinolines (Dpyr) were measured, and the results were normalized to creatinine. Age-related changes in cross-links excretion were observed. The levels decreased with age, and a peak of excretion was shown at the beginning of adolescence. Prepubertal levels of all the markers were four- to five-fold higher than in adults, and they decreased towards adult levels in late puberty. Girls had significantly higher levels of all biochemical markers than boys at pubertal stage 2. We also observed a remarkable effect of puberty on the levels of bone degradation products that was independent of age and gender. Our results indicate that bone resorption is high in children relative to that in adults, and that urinary levels of NTx, Pyr, and Dpyr change as a function of age, gender, and puberty.