Vaccination coverage for infants with CHD is unknown, yet these patients are at high risk for morbidity and mortality associated with vaccine-preventable illnesses. We determined vaccination rates for this population and identified predictors of undervaccination. We prospectively enrolled infants with CHD born between 1 January, 2012 and 31 December, 2015, seen in a single-centre cardiology clinic between 15 February, 2016 and 28 February, 2017. We assessed vaccination during the first year of life. Subjects who by age 1 year received all routine immunisations recommended during the first 6 months of life were considered fully vaccinated. We also evaluated influenza vaccination during subjects’ first eligible influenza season. We obtained immunisation histories from primary care providers and collected demographic and clinical data via a parent survey and chart review. We used multivariable logistic regression to identify predictors of undervaccination. Among 260 subjects, only 60% were fully vaccinated. Vaccination rates were lowest for influenza (64.6%), rotavirus (71.1%), and Haemophilus influenzae type b (79.3%). Cardiac surgery with cardiopulmonary bypass during the first year of life was associated with undervaccination (51.5% versus 76.4% fully vaccinated, adjusted odds ratio 2.1 [95% confidence interval 1.1–3.9]). Other predictors of undervaccination were out-of-state primary care (adjusted odds ratio 2.7 [1.5–4.9]), multiple comorbidities (≥2 versus 0–1, adjusted odds ratio 2.0 [1.1–3.6]), and hospitalisation for >25% of the first year of life (>25% versus ≤25%, adjusted odds ratio 2.1 [1.1–3.9]). Targeted quality improvement initiatives focused on improving vaccination coverage for these infants, especially surrounding cardiac surgery, are needed.