BACKGROUND: In recent years, the prevalence of non-communicable diseases (NCDs) has escalated. Evidence suggests that there are strong associations between nutrition in early life and the risk of disease in adulthood. This manuscript describes the study protocol of the First United Arab Emirates National Representative Birth Cohort Study (UAE-BCS), with the objective of investigating nutrition and lifestyle factors in the first 1,000 days of life. The main aims of the study are (1) to address critical issues relating to mother and child nutrition and their effect on growth and development, (2) to profile maternal nutrition, child growth, health, and development outcomes in early life, and (3) to study the associations between these factors among the Emirati population in the UAE. METHODS/DESIGN: In this study, a multidisciplinary team of researchers was established including credible researchers from the UAE, Lebanon, Australia, and the United Kingdom to launch the First United Arab Emirates 3-year birth cohort study. We aim to recruit 260 pregnant Emirati women within their first trimester, which is defined by the study as from 8 to 12 weeks pregnant, from obstetrics and gynecology clinics in the UAE. Participants will be recruited via face-to-face interviews and will receive a total of 11 visits with 1 visit in each trimester of pregnancy and 8 visits after delivery. Maternal data collection includes, socio-demographic and lifestyle factors, dietary intake, anthropometric measurements, physical activity, maternal psychological state, and blood samples for biochemical analysis. Post-partum, visits will take place when the child is 0.5, 4, 6, 9, 12, 18, and 24 months old, with data collection including infant anthropometric measurements, young child feeding practices, dietary intake, supplement use and the eating environment at home, as well as all maternal data collection described above, apart from blood samples. Additional data collection for the child includes early child developmental assessments taking place at three timepoints: (1) within 2 weeks of birth, (2) at 10-14 months and (3) at 22-26 months of age. Early child developmental assessments for the infant include vision, hearing, cognition, motor skills, social-emotional reactivity, neurodevelopmental, and sleep assessments. DISCUSSION: The United Arab Emirates Birth Cohort study protocol provides a standardized model of data collection methods for collaboration among the multisectoral teams within the United Arab Emirates to enrich the quality and research efficiency in early nutrition, thereby enhancing the health of mothers, infants, and children.