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Abstract Objective To determine uptake of influenza vaccination in children with special risk medical conditions (SRMC) and to explore associations with vaccination. Design Cross-sectional study. Setting/participants Parents of children with a SRMC attending either outpatient department clinics or being an inpatient at the Women's and Children's Hospital (WCH), Adelaide, Australia from September 2015 to February 2016 were recruited using convenience sampling. Methods Data were collected using a face-to-face survey. Influenza vaccination was verified with providers. Characteristics associated with uptake were explored using univariable and multivariable analyses. Results There were 410 participants with complete data. Confirmed influenza vaccination at least once in the last two years was 50%, annual uptake was 32.8%. 63.9% of parents were aware of the vaccination recommendation and 57.9% had been recommended by a specialist or general practitioner (GP). Characteristics strongly associated with uptake included: receiving a recommendation from a specialist or GP and having a parent receive the influenza vaccine annually. Conclusions Despite a long standing funded program, influenza vaccination uptake in children with SRMC is suboptimal. Parental vaccination behaviour, along with medical practitioner recommendation, particularly specialist recommendation, appear to be key influences in facilitating vaccination. Potential interventions could target the family rather than just the individual child. Understanding the barriers to recommendation from the perspective of general medical practitioners and specialists who treat these children is needed. [ABSTRACT FROM AUTHOR]