Impaired mitochondrial function and structure and intramyocellular lipid (IMCL) accumulation have been associated with obesity and Type 2 diabetes. We examined whether endurance exercise training and sex influenced IMCL and mitochondrial morphology using electron microscopy, whole-body substrate use, and mitochondrial enzyme activity. Untrained men ( n = 5) and women ( n = 7) were tested before and after 7 wk of endurance exercise training. Testing included 90 min of cycle ergometry at 60% V̇o2 peak with preexercise muscle biopsies analyzed for IMCL and mitochondrial size/area using electron microscopy and short-chain β-hydroxyacyl-CoA dehydrogenase (SCHAD) and citrate synthase (CS) enzyme activity. Training increased the mean lipid area density ( P = 0.090), the number of IMCL droplets ( P = 0.055), the number of IMCL droplets in contact with mitochondria ( P = 0.010), the total mitochondrial area ( P < 0.001), and the size of individual mitochondrial fragments ( P = 0.006). Women had higher mean lipid area density ( P = 0.030) and number of IMCL droplets ( P = 0.002) before and after training, but higher individual IMCL area only before training ( P = 0.013), compared with men. Women oxidized more fat ( P = 0.027) and less carbohydrate ( P = 0.032) throughout the study. Training increased V̇o2 peak ( P < 0.001), %fat oxidation ( P = 0.018), SCHAD activity ( P = 0.003), and CS activity ( P = 0.042). In summary, endurance exercise training increased IMCL area density due to an increase in the number of lipid droplets, whereas the increase in total mitochondrial area was due to an increase in the size of individual mitochondrial fragments. In addition, women have higher IMCL content compared with men due mainly to a greater number of individual droplets. Finally, endurance exercise training increased the proportion of IMCL in physical contact with mitochondria.