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The evidence regarding associations between intensity-specific physical activity and adiposity in young children is inconclusive. The aim of this study was to determine the multivariate physical activity intensity signatures associated with body mass index and waist-to-height ratio in children aged 3–5 years. A sample of 1003 Norwegian preschool children (mean age 4.3 years, 51 % boys) from the Active Learning Norwegian Preschool(er)s study provided data on physical activity (ActiGraph GT3X+), body mass index, and waist-to-height ratio during 2019–2020. Multivariate pattern analysis was used to determine associations between the triaxial intensity spectrum (0–99 to ≥15,000 counts per minute) and the outcomes. We found significant associations for physical activity with body mass index and waist-to-height ratio (explained variances = 10.8 and 11.5 %, respectively). For the vertical axis, associations were negative for time spent sedentary (0–99 counts per minute) and positive for time spent in lower intensities (100–2999 counts per minute) for both outcomes, whereas associations for vigorous intensities (≥4000 counts per minute) differed for body mass index (no associations) and waist-to-height ratio (negative associations). Association patterns for body mass index and waist-to-height ratio were rather similar, but the stronger associations with vigorous physical activity intensities for waist-to-height ratio suggest that waist-to-height ratio might better capture adiposity resulting from inactivity than body mass index.