Tetralogy of Fallot (TOF) is a common congenital heart defect (CHD). However, the genetic causes are largely unknown. Blood vessel epicardial substance (BVES) is postulated to play a role in embryonic development, and we previously found that the expression of BVES is upregulation in patients with congenital septal defect and that BVES participates in cardiocyte differentiation. We hypothesized that BVES is a candidate gene of TOF. In the present study, the entire coding sequence and splice junctions of BVES were sequenced in 114 unrelated patients with TOF and 400 unrelated healthy individuals used as controls. The functional effects of the exon mutant BVES were characterized in contrast to its wild-type counterpart using a luciferase reporter assay system. Four novel BVES mutations (c.166T>C, c.909C>T, c.540-80C>T, c.958+30A>G) were identified in patients with TOF but not in the 400 controls. Functional analysis indicated that the c.166T>C mutation of BVES was associated with an increased transcriptional activity. This finding suggests that BVES as a novel TOF gene may provide further insight into the molecular mechanisms involved in TOF.