To determine whether cardiac catheterisation procedures for low birth weight neonates ≤2.5 kg carries a greater risk of complications compared with neonates >2.5 kg, we conducted a single-centre retrospective case–control study. From 01/03 to 01/09, 46 consecutive neonates <2.5 kg at the time of cardiac catheterisation were identified. For each low birth weight case, three control patients >2.5 kg were randomly selected from our heart centre database during the same time period. Data included demographic characteristics, type of intervention, fluoroscopy time, contrast volume, pre- and post-blood urea nitrogen to creatinine ratio, physician performing procedure, procedural risk category, and all major and minor complications. The overall incidence of complications was higher in neonates ≤2.5 kg compared with neonates >2.5 kg (34.8% versus 17.6%, p = 0.023) because of a greater proportion of minor complications (34.8% versus 16.9%, p = 0.021). When specific minor complications were stratified, there was a greater incidence of hypotension requiring intravenous fluids in neonates ≤2.5 kg (6.5% versus 0%, p = 0.015). After controlling for physician performing procedure and risk category, neonates ≤2.5 kg remained at a higher risk for any complication (adjusted odds ratio = 3.2, 95% confidence interval 1.4–7.2, p = 0.005). The percentage of neonates having at least one major complication was not higher in the ≤2.5-kg group (2.2% versus 2.2%). No procedural deaths occurred in either group.