It is unknown whether relationships detected between physical activity intensity and health differ according to accelerometer thresholds used [sample-specific thresholds (SSTs), published thresholds (PTs) or the individualized activity-related time equivalent (ArteACC)]. SSTs were developed through ActiGraph calibration in 52 boys, aged 8-10 years. The boys subsequently wore an ActiGraph for seven days. SSTs, PTs and ArteACC for moderate (MPA) and vigorous (VPA) activity were applied. Waist circumference (WC), peak oxygen consumption (VO_2peak) and blood pressure were assessed. After applying SSTs, 48.9% of boys achieved 60+ minutes of daily MVPA, compared with 8.5% with PTs and 100% with ArteACC. MPA and VPA were correlated with WC and VO_2peak, regardless of whether PTs or SSTs were used (WC: MPA r = -0.37 to -0.43; VO_2peak: r = 0.34 to 0.39, p < 0.05). With ArteACC, only VPA was correlated with WC (r = -0.39, p < 0.01) and VO_2peak (r = 0.35, p < 0.05). Relationships with blood pressure were statistically non-significant. Although estimates of the quantity of activity differed according to thresholds used, relationships detected with health were consistent regardless of whether SSTs or PTs were employed. There was no advantage of using SSTs or individualized thresholds. Researchers are encouraged to use PTs to ensure greater comparability between studies.