The measurement of heart rate variability (HRV) is often considered a convenient non-invasive assessment tool for monitoring individual adaptation to training. Decreases and increases in vagal-derived indices of HRV have been suggested to indicate negative and positive adaptations, respectively, to endurance training regimens. However, much of the research in this area has involved recreational and well-trained athletes, with the small number of studies conducted in elite athletes revealing equivocal outcomes. For example, in elite athletes, studies have revealed both increases and decreases in HRV to be associated with negative adaptation. Additionally, signs of positive adaptation, such as increases in cardiorespiratory fitness, have been observed with atypical concomitant decreases in HRV. As such, practical ways by which HRV can be used to monitor training status in elites are yet to be established. This article addresses the current literature that has assessed changes in HRV in response to training loads and the likely positive and negative adaptations shown. We reveal limitations with respect to how the measurement of HRV has been interpreted to assess positive and negative adaptation to endurance training regimens and subsequent physical performance. We offer solutions to some of the methodological issues associated with using HRV as a day-to-day monitoring tool. These include the use of appropriate averaging techniques, and the use of specific HRV indices to overcome the issue of HRV saturation in elite athletes (i.e., reductions in HRV despite decreases in resting heart rate). Finally, we provide examples in Olympic and World Champion athletes showing how these indices can be practically applied to assess training status and readiness to perform in the period leading up to a pinnacle event. The paper reveals how longitudinal HRV monitoring in elites is required to understand their unique individual HRV fingerprint. For the first time, we demonstrate how increases and decreases in HRV relate to changes in fitness and freshness, respectively, in elite athletes.