QUESTIONS: In Switzerland, the screening of neonates for congenital heart defects (CHD) by using pulse oximetry (PO) on the first day of life was recommended in 2005. We assessed the current practice of Swiss maternity units regarding PO screening to define the actual screening rate in Switzerland and to detect possible difficulties in the implementation of this screening. METHODS: This descriptive study was conducted by means of a standardized questionnaire that was sent to all Swiss maternity units. RESULTS: The response rate was 100%. 76% of the units perform regular PO screening and, on the basis of the number of births for 2007, this means that 85% of newborns in Switzerland undergo screening. Although units which do not perform PO screening include every category of maternity unit, the screening is performed to a significantly lower extent in birthing centres than in hospitals (p <0.001). The number of unscreened neonates was 5398 within small units (<1000 births per year) while it was 6137 within large units (>1000 births per year). The main reasons for not performing PO screening are financial factors and the belief that clinical signs are sufficient for the detection of CHD. CONCLUSIONS: Greater effort is needed to implement a nationwide PO screening program for CHD. Special attention should be paid to birthing centres given their limited capacity to treat newborns with critical CHD.