BACKGROUND Ventricular septation is an option for surgical correlation of double-inlet or common-inlet left ventricle. However, the surgical risk factors of ventricular septation remain unknown. METHODS Twenty-three patients with double-inlet or common-inlet left ventricle underwent ventricular septation. Preoperative data were compared between the survivors (n = 18) and the nonsurvivors (n = 5) to assess surgical risk factors. RESULTS There were two early deaths (9.5%) and three late deaths (14.3%). Nonsurvivors of ventricular septation were significantly older at the time of operation (14.0 +/- 6.0 versus 7.0 +/- 5.4 years; p < 0.05) and had greater left ventricular mass (383% +/- 100% versus 206% +/- 57% of normal predicted value; p < 0.005) and greater left ventricular mass to left ventricular end-diastolic volume ratio (1.84% +/- 1.18% versus 0.77% +/- 0.17%/% of normal predicted value; p < 0.005). Univariate logistic regression analysis also revealed age at operation (p < 0.05) and mass/end-diastolic volume ratio (p < 0.05) as significant risk factors for death after operation. Multivariate regression analysis revealed that age at operation positively influenced increased mass/end-diastolic volume ratio (p < 0.001). These findings indicated that ventricular hypertrophy was one of the risk factors for ventricular septation, which had a tendency to progress with age. CONCLUSIONS Early operation before progression of ventricular hypertrophy is recommended in patients with double-inlet or common-inlet left ventricle who have suitable anatomy for the ventricular septation procedure.