Previous research has shown that two populations of mitochondria with different metabolic properties exist in human skeletal muscle. Recent research has shown that the regional distribution of succinate dehydrogenase (SDH) in single muscle fibres is altered with moderate intensity endurance training. Based on this information, we tested the hypothesis that the regional distribution of mitochondria would be altered following sustained high intensity endurance training. PURPOSE The purpose of this study was to examine the changes in the subsarcolemmal (SSM) and intermyofibrillar (IMF) mitochondria as represented by changes in SDH activity. METHODS Eight (2 female, 6 male) trained cyclists (VO2max = 60.7 mL.kg−1·min−1) performed eight weeks of high intensity endurance training for 60 minutes × 5d.wk−1 at 80–85% VO2max. Pre- and post-training muscle biopsy samples were taken from the vastus lateralis, and then immediately frozen in isopentane until analyzed histochemically for SDH activity. Frozen tissue sections (6μm) were incubated and then analyzed using a computer-enhanced image analysis system which digitized selected fibres (18–75) to represent SDH activity as an optical density. Concentric rings (pixel width 0.75μm) were partitioned from the outside layer (SSM, <5.25μm) to the inside layer (IMF, > 6.00μm). Based on myofibrillar ATPase staining, Type I and Type II fibres were identified. RESULTS The results showed that significant changes (ANOVA, p < 0.05) occurred for all analyses performed, both pre- vs. post-training for fibre types, and between SSM and IMF mitochondria. SDH activity increased significantly in Type II (71.7%) vs. Type I (28.3%) over training. The greatest increases in the mitochondrial activity occurred in the SSM (54.6%) vs. IMF (45.4%). However, the greatest increase in SDH activity occurrred in the IMF mitochondria of Type II fibres (39.7%). CONCLUSIONS These data demonstrated that high intensity endurance training can elicit selective adaptations in the metabolic profile of different fibre types in single muscle fibres, and that regional differences in SDH activity can occur.