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The purpose of this article was to describe and to apply a comprehensive set of guiding principles in the selection of measurement instruments for a longitudinal epidemiologic study focusing on functioning using the International Classification of Functioning, Disability, and Health (ICF) as reference framework. Based on the literature, the ICF linkage rules, and the definition of ICF categories to be measured, the following guiding principles for selecting measurement instruments are defined: redundancy, efficiency, level of detail of information, comparability, feasibility, and truth and discrimination. Examples illustrate that the application of guiding principles allows for a systematic and reasoned process of measurement instrument selection and thus offers a potential solution for the multifaceted challenges that one encounters in the selection of measurement instruments. It is transparently demonstrated how the ICF linkage rules enable researchers to address issues such as efficiency, comparability, and redundancy and how the definition of a set of ICF categories to be measured allows assessing inefficiencies in measurement instruments. Because of the ICF linkage rules and the definition of ICF categories to be measured, new guiding principles for selecting measurement instruments emerge. The main challenges lie in the difficulty to quantify and prioritize the applicability of guiding principles and the fact that they strongly interact. Notably, the prioritization and application of guiding principles must be defined considering the specific characteristics and aims of the specific study.