The findings of previous studies investigating the strength of the relationships between the percentages of maximal heart rate (%HRmax), heart rate reserve (%HRR), maximal oxygen uptake (%VO2max), and oxygen uptake reserve (%VO2R) have been equivocal. This inconsistency between studies could largely be due to differences in methodology. The purpose of this study was therefore to determine whether different VO2max test protocols and resting VO2 assessment influence the relationships between the %HRmax, %HRR, %VO2max, and %VO2R. Thirty-three young men performed maximal treadmill protocols (ramp, Bruce) to assess HRmax and VO2max. Resting VO2 was assessed as follows: a) resting VO2standard, using strict criteria (24 h exercise abstention, alcohol, soft drinks, or caffeine; 8 h fasting; 30 min assessment); b) resting VO2sitting and; c) resting VO2standing (both 5 min before exercise testing). The %HRR was closer to %VO2max than to %VO2R, especially in the ramp protocol (p < 0.001). In the Bruce protocol, relationships were closer to the identity line, and there was no significant difference between %HRR and %VO2max, or %VO2R. The VO2max was significantly higher in the ramp protocol compared to the Bruce protocol (p < 0.001). In both protocols resting VO2 assessment produced no significant difference in the intercepts and slopes of the %HRR-%VO2R relationships obtained from individual regression models. The %VO2R calculated using resting VO2standard was closer to %HRR compared to VO2sitting and VO2standing. The premise that %HRR is more strongly related to %VO2R than to %VO2max was not confirmed. Methodological differences should be considered when interpreting previous studies investigating %HRmax, %HRR, %VO2max, and %VO2R relationships.