Background The configuration of the interventricular septum can affect the function of the tricuspid valve in patients with congenitally corrected transposition of the great arteries who have a systemically functioning right ventricle. Altering septal configuration by addressing a dysfunctional conduit placed between the left ventricle (LV) and the pulmonary artery (PA) in these patients can impact septal configuration and competency of the tricuspid valve. Methods In 38 patients with an LV to PA conduit, we evaluated relationships between conduit function, RV geometry, and tricuspid valve function, and compared these variables before and after conduit intervention. Results Median age at conduit implant was 4.5 years (0.5 to 36) and median total follow-up was 12 years (2 to 22). Of the 38 patients, 23 (60%) underwent conduit intervention, a median of 7.5 years after implant. In 15 of these patients (65%) the degree of tricuspid regurgitation (TR) worsened, compared with only 2 patients (15%) in the non-intervention group (p < 0.001). Worsening TR was associated with the degree of change in RV and LV ventricular diameters, change in tricuspid annulus size and tethering distance, and the degree of septal shift, as reflected by the right ventricular sphericity index (all p 0.04). In 8 of 15 patients with more severe TR at follow-up, there was also progressive RV dysfunction. Conclusions Intervention for LV to PA conduit dysfunction may result in worsening TR and right ventricular function, likely due in part to altered septal shift due to changes in the interventricular pressure ratio. Management of LV to PA conduit dysfunction should take these findings into account.