A longitudinal field study was performed in order to characterize age-related changes of ultrasound measurements, biochemical markers, growth factors and other metabolic variables related with bone metabolism in the young horse. Twenty-seven Lusitano foals (11 colts, 16 fillies), born and raised on four stud-farms, were periodically assessed from birth to 36 months of age. Quantitative ultrasound measurements were performed on the mid-section of the right third metacarpal bone (dorsal and lateral regions) and blood samples were collected for determination of osteocalcin (Oc), bone alkaline phosphatase (BALP), insulin-like growth factor I (IGF-I), leptin, insulin, glucose, parathyroid hormone (PTH), calcium, phosphorus and magnesium plasma concentrations. Data were analyzed using a repeated measures model that includes the fixed effects of time (days of age), time × time, sex, foaling season, their interactions, and the farm as a random effect. Speed of sound values increased with age (P < 0.001) for both bone regions, but this increase was more pronounced in colts than in fillies (age × sex interaction, P < 0.01). Bone biochemical markers, IGF-I, leptin, glucose and plasma mineral concentrations changed markedly with age (P < 0.01), and a statistically significant age × sex interaction was also observed for leptin (P < 0.01). Leptin and Oc plasma concentrations were negatively correlated (r = −0.098; P < 0.05). In this longitudinal analysis, insulin and PTH concentrations were not specifically influenced by age, sex or foaling season. The present study provided information on a sequence of physiologic events throughout the first three years of life of young horses, under field conditions. Therefore, this detailed characterization of variables involved in skeletal development during such a long period, may become useful for further investigation, even in other breeds.