Background: Children with congenital heart disease require repeated catheterization. Anesthetic management influences the procedure and may influence outcome; however, data and recommendations are lacking for infants. We studied the influence of sedation versus general anesthesia (GA) on adverse events during catheterization for children <2 years old. Methods: We conducted a monocentric, retrospective study of all catheterization procedures (2008–2013). High-severity adverse event (HSAE) rates were compared using propensity-score-adjusted models, including pre- and intra-procedural variables. Results: 803 cases (619 patients) (368 (46%) GA, 435 (54%) sedation) with a mean age of 6.9 ± 6.1 months were studied. The conversion rate (GA after sedation) was 18 (4%). Hospital stay was 4.9 ± 4.0 and 4.1 ± 2.5 (p = 0.01) after GA or sedation, respectively. HSAE occurred in 75 (20%) versus 40 (9%) (p < 0.01) in GA versus sedation procedures, respectively. Risk factors (multivariable analysis) were older patients (p = 0.05), smaller weights (p < 0.01), palliated status (OR 3.2 [1.2–8.9], p = 0.02), two-ventricle physiology (OR 7.3 [2.7–20.2], p < 0.01), cyanosis (OR 4.6 [2.2–9.8], p < 0.01), pulmonary hypertension (OR 5.6 [2.0–15.5], p < 0.01), interventional catheterization (OR 1.8 [1.1–3.2], p = 0.02) and procedure-type risk category 4 (OR 28.9 [1.8–455.1], p = 0.02). Sedation did not increase the events rate and decreased the requirement for hemodynamic support (OR 5.2 [2.2–12.0], p < 0.01). Conclusion: Sedation versus GA for cardiac catheterization in children <2 years old is safe and effective with regard to HSAE. Sedation also decreases the requirement for hemodynamic support. Paradoxical effects (older age and two-ventricle physiology) on risk have been found for this specific age cluster.