Fourteen 3-week-old Sprague-Dawley rats were housed in pairs in standard cages (5 controls) and in individual cages with a running wheel. Four of these rats had run 27-36 km/week (low training - LT) and 5 had run 56-92 km/week (high training - HT). After 4 weeks, the rats were euthanized and Achilles tendons were fixed for electron microscopy. The ultrastructural distribution of cartilage oligomeric matrix protein (COMP) and thrombospondin (TSP)-4 and collagen fibril thickness in two different extracellular compartments were studied. The immunolabeling of COMP decreased with longer running distance and was significantly lower in both the pericellular (p = 0.009) and interterritorial (p = 0.03) compartments of the HT rats compared with the controls. TSP-4 immunolabeling was higher in the pericellular compared with the interterritorial compartments in all rats (p = 0.013) but was not correlated with COMP immunolabeling. No alterations in collagen fibril size were found in relation to running; however, the gold markers representing COMP and TSP-4 were mostly found at the dark bands, representing the gap region of the fibril.