Accurate and easy-to-use methods to assess free-living energy expenditure in response to physical activity in young children are scarce. In the present study, we evaluated the capacity of (1) 4 d recordings obtained using the Actiheart (mean heart rate (mHR) and mean activity counts (mAC)) to provide assessments of total energy expenditure (TEE) and activity energy expenditure (AEE) and (2) a 7 d activity diary to provide assessments of physical activity levels (PAL) using three sets of metabolic equivalent (MET) values (PALTorun, PALAdolph and PALAinsworth) in forty-four and thirty-one healthy Swedish children aged 1·5 and 3 years, respectively. Reference TEE, PALref and AEE were measured using criterion methods, i.e. the doubly labelled water method and indirect calorimetry. At 1·5 years of age, mHR explained 8 % (P= 0·006) of the variation in TEE above that explained by fat mass and fat-free mass. At 3 years of age, mHR and mAC explained 8 (P= 0·004) and 6 (P= 0·03) % of the variation in TEE and AEE, respectively, above that explained by fat mass and fat-free mass. At 1·5 and 3 years of age, average PALAinsworth values were 1·44 and 1·59, respectively, and not significantly different from PALref values (1·39 and 1·61, respectively). By contrast, average PALTorun (1·5 and 3 years) and PALAdolph (3 years) values were lower (P< 0·05) than the corresponding PALref values. In conclusion, at both ages, Actiheart recordings explained a small but significant fraction of free-living energy expenditure above that explained by body composition variables, and our activity diary produced mean PAL values in agreement with reference values when using MET values published by Ainsworth.