Background <p>Robust oral health data collection in birth cohort studies is needed to understand the oral microbiome in relation to oral and general health.</p> Objective <p>The aim of this paper is to describe the collection of oral health data in toddlers participating in a birth cohort focussing on microbiome development. Hereby, we aim to support the interpretation of variance in microbiome data.</p> Methods <p>The Amsterdam Infant Microbiome Study (AIMS, <i>n</i> = ~500) is a longitudinal prospective birth cohort assessing microbiota, general health status, demographics, (oral) health behaviour and dietary behaviour in children from birth up to three years. The Oral Health Study (OHS) is a sub-study of AIMS, assessing the oral health of children and their mothers. From the mothers, data on periodontal health (clinical attachment loss, gingival bleeding), oral hygiene (dental plaque, calculus) and dental caries (DMFS) is collected. In children, data on caries prevalence (ICDAS) and infection (pufa), oral hygiene (dental plaque, calculus), Obstructive Sleep Apnoea (OSA), oromuscular function, and bitter taste sensitivity are collected.</p> Results <p>Enrolment in OHS started in October 2022 and is planned to continue up to December 2028. In October 2024, 64 mother-child pairs were enroled in the study.</p> Conclusions <p>Data collection is expected to be completed by January 2028. Results will be shared at international conferences and via peer-reviewed publications.</p>