Background: Interstitial deletions within the long arm of chromosome 2, involving the 2q31q33 region, are rare but are known to be associated with delays in development, behavioral problems, facial dysmorphism and various hand/foot anomalies. Case presentation: Here, we describe a case with an interstitial 2q31.3.q32.2 deletion, presenting the previously described phenotype, exhibiting fibromyxoid degeneration of the aortic valve in addition to previously described clinical features. Conclusion: Interstitial deletion in chromosome 2q31.2q32.3 might be associated to a fibromyxoid degeneration of valvular leaflets generating regurgitation. Patients diagnosed with this mutation may require investigation to rule out a valvular disease.