Despite much progress with physical activity assessment, the limitations concerning the accurate measurement of physical activity are often amplified in young people due to the cognitive, physiological, and biomechanical changes that occur during natural growth as well as a more intermittent pattern of habitual physical activity in youth compared to adults. This mini-review describes and compares methods to assess habitual physical activity in youth and discusses main issues regarding the use and interpretation of data collected with these techniques. Self-report instruments and movement sensing are currently the most frequently used methods for the assessment of physical activity in epidemiological research; others include heart rate monitoring and multi-sensor systems. Habitual energy expenditure can be estimated from these input measures with varying degree of uncertainty. Non-linear modeling techniques, using accelerometry perhaps in combination with physiological parameters like heart rate or temperature have the greatest potential for increasing the prediction accuracy of habitual physical activity energy expenditure. Although multi-sensor systems may be more accurate, this must be balanced against feasibility, a balance which shifts with technological and scientific advances and should be considered at the beginning of every new study.