BackgroundInterfractional organ position variation might differ for abdominal organs and this could have consequences for defining safety margins. Therefore, the purpose of this study is to quantify interfractional position variations of abdominal organs in children in order to investigate possible correlations between abdominal organs and determine whether position variation is location-dependent.MethodsFor 20 children (2.2–17.8 years), we retrospectively analyzed 113 CBCTs acquired during the treatment course, which were registered to the reference CT to assess interfractional position variation of the liver, spleen, kidneys, and both diaphragm domes. Organ position variation was assessed in three orthogonal directions and relative to the bony anatomy. Diaphragm dome position variation was assessed in the cranial-caudal (CC) direction only. We investigated possible correlations between position variations of the organs (Spearman’s correlation test, ρ), and tested if organ position variations in the CC direction are related to the diaphragm dome position variations (linear regression analysis, R2) (both tests: significance level p < 0.05). Differences of variations of systematic (∑) and random errors (σ) between organs were tested (Bonferroni significance level p < 0.004).ResultsIn all directions, correlations between liver and spleen position variations, and between right and left kidney position variations were weak (ρ ≤ 0.43). In the CC direction, the position variations of the right and left diaphragm domes were significantly, and stronger, correlated with position variations of the liver (R2 = 0.55) and spleen (R2 = 0.63), respectively, compared to the right (R2 = 0.00) and left kidney (R2 = 0.25). Differences in ∑ and σ between all organs were small and insignificant.ConclusionsNo (strong) correlations between interfractional position variations of abdominal organs in children were observed. From present results, we concluded that diaphragm dome position variations could be more representative for superiorly located abdominal (liver, spleen) organ position variations than for inferiorly located (kidneys) organ position variations. Differences of systematic and random errors between abdominal organs were small, suggesting that for margin definitions, there was insufficient evidence of a dependence of organ position variation on anatomical location.Electronic supplementary materialThe online version of this article (10.1186/s13014-018-1108-9) contains supplementary material, which is available to authorized users.