BACKGROUND: Childhood obesity tracks into adulthood with detrimental effects on health. We aimed to examine the relationships of diet in childcare settings and daily physical activity (PA) of preschoolers with body mass index z-score (z-BMI). METHODS: We conducted a cross-sectional study of 150 children aged 2-4-years participating in the Nutrition and Physical Activity Self-Assessment for Child Care (NAP SACC) UK study to examine the associations of their diet in childcare settings and daily PA with z-BMI. Dietary intake was observed and recorded by fieldworkers using a validated tick-list food questionnaire and diet quality was assessed based on adherence to Children's Food Trust (CFT) guidelines. PA was measured using accelerometers. We derived z-BMI scores using the UK 1990 and International Obesity Taskforce growth reference charts. Multilevel regression models were used to estimate associations between diet and PA with z-BMI separately, adjusted for age, gender, ethnicity, parental education level and clustering. RESULTS: Among children who consumed one main meal or snack at childcare, 34.4% and 74.3% met the standards on fruits and vegetables and high sugar or fat snacks, respectively. Adherence to CFT guidelines was not associated with zBMI. Only 11.4% of children met recommended UK guidelines of three hours per day of physical activity. Minutes spent in light PA (β = 0.08, 95% CI = 0.01, 0.15) and active time (β = 0.07, 95% CI = 0.01, 0.12) were positively associated with UK 1990 zBMI scores. CONCLUSIONS: The low proportion of children meeting the standards on fruits and vegetables and high sugar or fat snacks and recommended physical activity levels highlight the need for more work to support nurseries and parents to improve preschool children's diet and activity. In our exploratory analyses, we found children with higher zBMI were more physically active which could be attributed to fat-free mass or chance finding and so requires replication in a larger study. TRIAL REGISTRATION: ISRCTN16287377 . Registered 12 June 2014.