Abstract Study question Is the distribution of abdominal visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) comparable between children following assisted reproduction and natural conception (NC)? Summary answer Children following frozen embryo transfer (FET) have significantly lower VAT/SAT-ratio than children following NC. However, this is not believed to be clinically important. What is known already It is well-established that an adverse distribution of the abdominal adipose tissue with high VAT/SAT-ratio increases the risk of cardiometabolic diseases, hence the VAT/SAT-ratio is closely related to the metabolic profile. Children conceived after FET and fresh embryo transfer (Fresh-ET) are at risk of being born large-for-gestational-age (LGA) and small-for-gestational-age (SGA), respectively. Both, being born LGA and SGA, increases the risk of obesity in later life. To the best of our knowledge, no studies have reported the VAT/SAT-ratio in children following assisted reproductive technology (ART) (both FET and Fresh-ET). Study design, size, duration Prospective observational cohort study including 150 singletons aged 7- to 10-years old conceived after FET (n = 50), Fresh-ET (n = 50) and NC (n = 50). All children were born in Eastern Denmark. The study is conducted between November 2018 and August 2020. Participants/materials, setting, methods This is a substudy af the “Health in Childhood following Assisted Reproductive Technology” (HiCART) study. The children underwent abdominal magnetic resonance imaging (MRI) for the quantification of abdominal adipose tissue along with measurements of anthropometric measurements, blood pressure, fasting blood samples and Dual-energy X-ray Absorptiometry (DXA) scan. The volumes of VAT and SAT were semi-automatically quantified blinded for the mode of conception. Multivariate linear regression analysis of the VAT/SAT-ratio was performed to adjust for confounders. Main results and the role of chance The VAT/SAT-ratio differed significantly between the three groups (mean SD; FET 0.26 (0.08), Fresh-ET 0.29 (0.07), NC 0.30 (0.08), ANOVA, p = 0.014). Pairwise comparison revealed that children conceived after FET had significantly lower VAT/SAT-ratio as compared to children conceived after NC (p = 0.007). In addition, children following FET tended to have lower VAT/SAT-ratio as compared to the Fresh-ET group (p = 0.059). Multivariate linear regression analysis of the VAT/SAT-ratio confirmed a lower VAT/SAT-ratio in FET after adjustment for potential confounding factors (child age and sex, maternal age at delivery and maternal BMI at pregnancy and child birth weight and BMI). Repeat-analysis of 20 MRI showed good intra-rater reliability of VAT and SAT quantifications. As previously reported in the HiCART studies, there were no differences between the groups in anthropometric measurements including body mass index (BMI), lean body mass, blood pressure or high-sensitivity C-reactive protein (hs-CRP). However, the level of triglycerides was found to be significantly higher in Fresh-ET compared to FET and NC (p = 0.028). Limitations, reasons for caution Selection bias cannot be excluded as only children from Eastern Denmark were invited. The observational nature of a cohort study prevents the establishment of causality. Wider implications of the findings Reassuringly, this study found no clinical important difference in abdominal adipose tissue between children following ART (both FET and Fresh-ET) and NC. However, future studies in larger cohorts are warranted. Trial registration number ClinicalTrials.gov identifier: NCT03719703