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Objective To evaluate time trends in the use of catheter and surgical procedures, and associated survival in isolated congenital shunt lesions. Methods Nationwide, retrospective observational study of the UK National Congenital Heart Disease Audit database from 2000 to 2016. Patients undergoing surgical or catheter procedures for atrial septal defect (including sinus venosus defect), patent foramen ovale, ventricular septal defect and patent arterial duct were included. Temporal changes in the frequency of procedures, and survival at 30 days and 1 year were determined. Results 40 911 procedures were performed, 16 604 surgical operations and 24 307 catheter-based interventions. Transcatheter procedures increased over time, overtaking surgical repair in 2003–2004, while the number of operations remained stable. Trends in interventions differed according to defect type and patient age. Catheter closure of atrial septal defects is now more common in children and adults, although surgical interventions have also increased. Patent foramen ovale closure in adults peaked in 2009–2010 before falling significantly since. Surgery remains the mainstay for ventricular septal defect in infants and children. Duct ligation is most common in neonates and infants, while transcatheter intervention is predominant in older children. Excluding duct ligation, survival following surgery was 99.4% and ≈98.7%, and following catheter interventions was 99.7% and ≈99.2%, at 30 days and 1 year, respectively. Conclusions Trends in catheter and surgical techniques for isolated congenital shunt lesions plot the evolution of the specialty over the last 16 years, reflecting changes in clinical guidelines, technology, expertise and reimbursement, with distinct patterns according to lesion and patient age.