PURPOSE: Using a novel technique of high-density surface electromyography (HDEMG) decomposition and motor unit (MU) tracking, we compared changes in the properties of vastus medialis (VM) and vastus lateralis (VL) MUs following endurance (END) and high-intensity interval training (HIIT). METHODS: Sixteen men were assigned to an END or HIIT group (n=8 each) and performed six training sessions over 14 days. Each session consisted of 8-12×60s intervals at 100% peak power output (PPO) separated by 75s of recovery (HIIT) or 90-120min continuous cycling at ~65% VO2peak (END). Pre and post intervention, participants performed: 1) incremental cycling to determine VO2peak and PPO and 2) maximal (MVC), submaximal (10, 30, 50 and 70% MVC) and sustained (until task failure at 30% MVC) isometric knee extensions while HDEMG signals were recorded from the VM and VL. EMG signals were decomposed (submaximal contractions) into individual MUs by convolutive blind source separation. Finally, MUs were tracked across sessions by semi-blind source separation. RESULTS: After training, END and HIIT improved VO2peak similarly (by 5.0 and 6.7%, respectively). The HIIT group showed enhanced maximal knee extension torque by ~7% (p=0.02) and was accompanied by an increase in discharge rate for high-threshold MUs (≥50% knee extension MVC) (p<0.05). In contrast, the END group increased their time to task failure by ~17%, but showed no change in MU discharge rates (p>0.05). CONCLUSIONS: HIIT and END induce different adjustments in MU discharge rate despite similar improvements in cardiopulmonary fitness. Moreover, the changes induced by HIIT are specific for high-threshold motor units. For the first time we show that HIIT and END induce specific neuromuscular adaptations, possibly related to differences in exercise load intensity and training volume.