This study aimed to compare the acute effects of hypertrophic (HYP) and maximum strength (MAX) loadings on heart rate variability (HRV) and to compare possible loading-specific alterations with other markers of recovery. Ten young men with strength training experience performed two leg press loadings (HYP: five times 10 repetitions at 70% of one repetition maximum (1RM) with 2 minutes inter-set rest; MAX: 15 times one repetition at 100% of 1RM with 3 minutes inter-set rest) in a randomized order. The root mean square of successive differences statistically decreased after both protocols (HYP: 65.7 +/- 26.6 ms to 23.9 +/- 18.7 ms, p = 0.026; MAX: 77.7 +/- 37.0 ms to 55.3 +/- 22.3 ms, p = 0.049), while the frequency domains of HRV remained statistically unaltered. The low frequency (LF) band statistically increased at 48h post-MAX only (p = 0.033). Maximal isometric voluntary contraction (MVC) statistically decreased after HYP (p = 0.026) and returned to baseline after 24h of recovery. Creatine kinase (CK) statistically increased above baseline at 1h post-loadings (HYP p = 0.028; MAX p = 0.020), returning to baseline at 24h post. Our findings indicate no distinct associations between changes in HRV and MVC or CK.