The amount and type of physical activity (PA) appropriate in youth for optimal health is still being discussed. The purpose of this study on 12-year-old preadolescents is to evaluate the association of two PA patterns, corresponding to different exercise intensities, with some health-related indexes. PA was evaluated by triaxial accelerometry in 67 student subjects, who were successively classified according to 1) their usual participation or not in moderately intense (> 4 metabolic equivalents, METs) activities (either in daily life or in leisure activities) for at least 210 min a week (4 M (210)); and 2) the habitual practice or not of more intense activities (> 6 METs) for at least 60 min a week (6 M (60)). Health-related indexes consisted of cardiopulmonary (maximum oxygen uptake, V.O 2max), muscular (lower limb strength) fitness parameters and vagal-related indexes of heart rate (HR) variability (HRV), such as the HF/(LF+HF) ratio (where HF and LF stand for high and low frequency power). HR was recorded in the supine position after 15 min of quiet rest, and HRV indexes were calculated in 5-min segments. Energy expenditure due to PA was not significantly associated with any health-related index. Reaching 4 M (210) was associated with both higher estimated V.O 2max (p < 0.05) and higher muscular strength indexes (p < 0.05) but not with enhanced HRV indexes. Subjects who reached 6 M (60) had higher estimated V.O2max (p < 0.05) and higher HF/(LF+HF) (p < 0.05). Our results show that regular moderately intense activities are sufficient to influence physical fitness but suggest that more intense activities are necessary to observe more favorable HRV vagal-related indexes.