BackgroundThinness during adolescence can increase the risk of adverse health outcomes across the life-course and impede development. There is limited research examining the prevalence and determinants of persistent adolescent thinness in the United Kingdom (UK). We used longitudinal cohort data to investigate determinants of persistent adolescent thinness.MethodsWe analyzed data from 7,740 participants in the UK Millennium Cohort Study at ages 9 months, 7, 11, 14 and 17 years. Persistent thinness was defined as thinness at ages 11, 14 and 17; thinness was defined as an age- and sex-adjusted Body Mass Index (BMI) of less than 18.5 kg/m2. In total, 4,036 participants, classified either as persistently thin or at a persistent healthy weight, were included in the analyses. Logistic regression analyses were conducted to examine associations between 16 risk factors and persistent adolescent thinness by sex.ResultsThe prevalence of persistent thinness among adolescents was 3.1% (n= 231). Among males (n= 115), persistent adolescent thinness was significantly associated with non-white ethnicity, low parental BMI, low birthweight, low breastfeeding duration, unintended pregnancy, and low maternal education. Among females (n= 116), persistent adolescent thinness was significantly associated with non-white ethnicity, low birthweight, low self-esteem, and low physical activity. However, after adjusting for all risk factors, only low maternal BMI (OR: 3.44; 95% CI:1.13, 10.5), low paternal BMI (OR: 22.2; 95% CI: 2.35, 209.6), unintended pregnancy (OR: 2.49; 95% CI: 1.11, 5.57) and low self-esteem (OR: 6.57; 95% CI: 1.46,29.7) remained significantly associated with persistent adolescent thinness among males. After adjustment for all risk factors, not reaching the recommended physical activity levels (OR: 4.22; 95% CI: 1.82, 9.75) remained significantly associated with persistent adolescent thinness among females. No appreciable associations were found between persistent adolescent thinness and sex, premature birth, smoking during pregnancy, income, maternal postnatal depression, mother-infant attachment or socio-emotional difficulties (p> 0.05).ConclusionPersistent adolescent thinness is not rare and appears to be associated with both physical and mental health factors, with some sex specific differences. Healthy weight initiatives should consider the full weight spectrum. Further research is required to understand thinness at a population level, including among those whose BMI changes during child and adolescent development.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-15850-1.