The present study investigated the effects of initial levels of cycling performance, peak oxygen uptake (O) and gross efficiency (GE) on the subsequent adaptations of these variables and their relationship following high-intensity training (HIT) designed to increase O in competitive cyclists. Sixty cyclists (O = 61 ± 6 mL kg min) were assigned a 12-week training program consisting of twenty-four supervised high-intensity interval training sessions and low intensity training. GE was calculated at 125, 175, and 225 W and performance was determined by mean power during a 40-min time-trial (Power). In addition to correlation analyses between initial level and pre- to post-intervention changes of the different variables, we compared these changes between four groups where participants were categorized with either low and/or high initial levels of O and GE. Average volume of high- and low-intensity training during the 12-week intervention was 1.5 ± 0.3 and 8.3 ± 2.7 h·week, respectively. Following the 12-week training period, there was a significant increase in absolute and body mass normalized O and Power ( < 0.05) and a significant decrease in GE ( < 0.05) for all athletes pooled. There was no change in body mass following the 12-week training period. We found a moderate negative correlation between initial level of O and the change in O following the training period ( = -0.32; < 0.05). A small negative correlation was also found between initial Power and its change following training both when expressed in absolute power and power normalized for body mass ( = -0.27 and -0.28; both < 0.05). A moderate negative correlation was also found between initial levels for GE and its change following training ( = -0.44; < 0.01). There were no differences between the four groups based on initial levels of O and GE in the response to training on O, GE, or Power (all > 0.12). In conclusion, the present findings suggest that there are statistically significant effects of initial levels of cycling performance and O and on the subsequent adaptations following a 12-week HIT program, but the small and moderate effects indicate limited influence on training practice.