Aortic regurgitation (AR) is a known complication of discrete subvalvar aortic stenosis (DSS), and its detection often triggers referral for surgery. However, risk factors for aortic valve dysfunction in children with DSS remain incompletely defined. The primary goal of this study was to determine independent risk factors for moderate or severe AR at mid-term follow-up in patients with DSS. Clinical records and echocardiograms of 220 patients with DSS (109 patients had DSS resection and 111 had no surgery) were analyzed. The primary outcome variable was AR grade (based on the width of the vena contracta) at latest follow-up. Age at diagnosis, gender, and duration of follow-up (median 7.2 years, range 1 to 20.4) did not differ significantly between medical and surgical patients. By multivariate analysis, independent risk factors for moderate to severe AR (n = 30) were older age at diagnosis of DSS (odds ratio [OR] for age ≥17 years 5.13, p = 0.024), previous balloon or surgical aortic valvuloplasty (OR 19.6, p <0.001), and a longer follow-up period (OR for 1-year increase 1.15, p = 0.032). Excluding patients with previous surgical or balloon aortic valvuloplasty, a higher maximal Doppler gradient was an independent risk factor for moderate to severe AR (OR for peak gradient ≥50 mm Hg 10.8, p = 0.001). Independent predictors of low-risk patients (none or trivial AR and peak gradient ≤30 mm Hg) included thin and mobile aortic valve leaflets (OR 7.86, p = 0.006) and an associated ventricular septal defect (OR 2.18, p = 0.019). These clinical and echocardiographic variables can be used to stratify risk of aortic valve dysfunction in patients with DSS and aid in timing of surgical resection.