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The purpose of this longitudinal in-field study was to evaluate the influence of exercise, age, and gender on superficial cortical bone of the third metacarpal bone (MC III) in young Thoroughbreds by measuring speed of sound (SOS) values with an axial transmission technique (Omnisense, Sunlight Ltd, Israel). Both MC III of 75 racehorses, 2 to 4 years old, were monitored with SOS measurements in 5- to 7-week intervals during a 9- month physical exercise period. Medical data and training programs (slow gallop, canter, and high-speed work) of each horse were recorded. SOS measurements began before 2-year-old horses started high-speed training. SOS values of the dorsal aspect of MC III were significantly lower in comparison with values obtained at the lateral and the medial aspect of MC III, and SOS values were inversely correlated with measurement cycles. Significant limb-associated differences in dorsal MC III SOS values were observed at measurement cycles 2, 3, and 4. SOS values obtained at the lateral and medial aspect of MC III increased with age. SOS values obtained at the dorsal aspect of MC III, decreased with age. Mares had significantly higher SOS values at the dorsal aspect of MC III, when compared with corresponding values in stallions. In 2-year-old Thoroughbreds SOS values of the dorsal MC III were significantly different between cycles 1 and 2, between cycles 3 and 4, and between cycles 4 and 5. Three-year-old horses showed significant differences between SOS values of the dorsal MC III obtained at cycles 3 and 4. Training intensities did not significantly influence SOS values. The results indicate that young exercising Thoroughbred racehorses have age-, gender-, and measurement-cycle-dependent variations in SOS values of MC III, which probably reflect adaptive variations in superficial cortical bone properties of MC III.