ObjectiveChildren with medical complexity (CMC) are among the most vulnerable patient groups. This study aimed to evaluate their prevalence and risk factors for medication misunderstanding and potential harm (PH) at discharge.Design and settingCross-sectional study at a tertiary care centre.Study populationCMC admitted at Medical University of Vienna between May 2018 and January 2019.InterventionCMC and caregivers underwent a structured interview at discharge; medication understanding and PH for adverse events were assessed by a hybrid approach.Main outcome measuresMedication misunderstanding rate; PH.ResultsFor 106 included children (median age 9.6 years), a median number of 5.0 (IQR 3.0–8.0) different medications were prescribed. 83 CMC (78.3%) demonstrated at least one misunderstanding, in 33 CMC (31.1%), potential harm was detected, 5 of them severe. Misunderstandings were associated with more medications (r=0.24, p=0.013), new prescriptions (r=0.23, p=0.019), quality of medication-related communication (r=−0.21, p=0.032), low level of education (p=0.013), low language skills (p=0.002) and migratory background (p=0.001). Relative risk of PH was 2.27 times increased (95% CI 1.23 to 4.22) with new medications, 2.14 times increased (95% CI 1.10 to 4.17) with migratory background.ConclusionDespite continuous care at a tertiary care centre and high level of subjective satisfaction, high prevalence of medication misunderstanding with relevant risk for PH was discovered in CMC and their caregivers. This demonstrates the need of interventions to improve patient safety, with stratification of medication-related communication for high-risk groups and a restructured discharge process focusing on detection of misunderstandings (‘unknown unknowns’).