Femoral arterial thrombosis (FAT) is a nonnegligible complication after cardiac catheterization (CC) in infancy. The aim of this study was to evaluate the impact of Doppler ultrasound (US) for diagnostic work-up after catheterization. We compared standard follow-up (FU) without Doppler US by relying on clinical signs of FAT with advanced FU using Doppler US of the femoral vessels. Between January and December 2009, we evaluated the rate of FAT in infants <12 months of age using a multicenter, prospective observational survey. We analysed 171 patients [mean age 4.1 ± 3.3 (SD) months; mean body weight 5.3 ± 1.8 kg] from 6 participating centres. The mean duration of catheter studies was 57.7 ± 38.0 min. The overall rate of FAT based on clinical diagnosis was 4.7 % and was comparable in both groups [3.4 % undergoing standard FU vs. 7.4 % undergoing advanced FU (p = 0.15)]. However, the overall rate of thrombosis as screened by Doppler US was greater at 7.1 %, especially in patients after advanced FU [18.5 % advanced vs. standard FU 1.7 % (p < 0.01)]. In conclusion, FAT remains a relevant and underestimated complication after catheterization in young infants when relying only on clinical signs of FAT. Therefore, to start effective treatment as soon as possible, we recommend Doppler US to be performed the day after CC.