Individual changes in resting heart rate variability (HRV) parameters were assessed in seven Polish cyclists during a training process consisting of: a six-week period (P1) of predominantly low- and moderate-intensity training (L-MIT) and a six-week period (P2) where the proportion of high-intensity interval training (HIT) increased. Daily recorded HRV parameters included high-frequency spectral power (HF), square root of the mean squared difference between successive normal-to-normal RR intervals (RMSSD), and standard deviation of normal-to-normal RR intervals (SDNN). In each training microcycle, the average values of HF(av), RMSSD(av), and SDNN(av) were calculated individually for each participant. In three cyclists, HF was higher in P2 compared to P1, whereas in one cyclist, HF was higher in P1 than in P2. Each of these four cyclists presented an individual correlation between the average daily duration HIT effort in training microcycles (HIT(av)) and HF(av). Cyclists with low baseline values of HRV parameters showed increased activity of the parasympathetic nervous system, while in the cyclist with high baseline values of HRV parameters, an opposite change was observed. In conclusion, changes in resting HRV parameters between period P1 and P2 can be individualised. In the investigated group, it was possible to predict how HRV would change as a result of training intensification on the basis of HRV baseline values.