This study aimed to compare sedentary time (SED) and intensity-specific physical activity (PA) estimates and the associations of SED and PA with body mass index (BMI) and waist circumference (WC) using three different sets of cut-points in preschool-aged children. A total of 751 children (4.7 ± 0.9 years, boys 52.7%) wore an ActiGraph GT3X+BT accelerometer on their hip for 7 days (24 h). Euclidean norm −1 G with negative values rounded to zero (ENMO) and activity counts from vertical axis (VACounts) and vector magnitude (VMCounts) were derived. Estimates of SED and light, moderate, vigorous, and moderate-to-vigorous PA (MVPA) were calculated for commonly used cut-points by Hildebrand et al., Butte et al., and Evenson et al. Furthermore, the prevalence of meeting the PA recommendation, 180 min/day of which at least 60 min/day being MVPA, were assessed for the cut-points. Multilevel mixed analysis was used to examine associations of SED and PA with BMI and WC. In accordance with the results, SED and PA intensity estimates differed largely across cut-points (i.e., SED = 22-341 min/day; light PA = 52-257 min/day; moderate PA = 5-18 min/day; vigorous PA = 7-17 min/day; MVPA = 13-35 min/day), and the prevalence of children meeting the PA recommendation varied from 4% to 70%. Associations of SED and PA with BMI or WC varied between the cut-points. Our results indicate that SED and PA estimates in preschool-aged children between studies using these This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.