This paper reviews the evidence behind the methodological decisions accelerometer users make when assessing habitual physical activity in children aged 0-5 years. The purpose of the review is to outline an evidence-guided protocol for using accelerometry in young children and to identify gaps in the evidence base where further investigation is required. Studies evaluating accelerometry methodologies in young children were reviewed in two age groups (0-2 years and 3-5 years) to examine: (i) which accelerometer should be used, (ii) where the accelerometer should be placed, (iii) which epoch should be used, (iv) how many days of monitoring are required, (v) how many minutes of monitoring per day are required, (vi) how data should be reduced, (vii) which cut-point definitions for identifying activity intensity should be used, and (viii) which physical activity outcomes should be reported and how. Critique of the available evidence provided a basis for the development of a recommended users protocol in 3-5-year olds, although several issues require further research. Because of the absence of methodological studies in children under 3 years, a protocol for the use of accelerometers in this age range could not be specified. Formative studies examining the utility, feasibility and validity of accelerometer-based physical activity assessments are required in children under 3 years of age. Recommendations for further research are outlined, based on the above findings, which, if undertaken, will enhance the accuracy of accelerometer-based assessments of habitual physical activity in young children.