Background: Niemann-Pick disease (NPD) is a rare autosomal recessive hereditary disease characterized by deficient activity of acid sphingomyelinase. Case presentation: We present a case of NPD type B with a unique compound heterozygosity for SMPD1 (NM_ 000543.4:c.[84delC];[96G > A]) in which both mutations that induce an early stop codon are located before the second in-frame initiation codon. The clinical presentation of the patient is compatible with NPD type B. She was initially diagnosed of Gaucher Disease, but her altered lipid profile led to a clinical suspicion of NPD. Combined high doses of atorvastatin and ezetimibe were given to treat the severe hypercholesterolemia. Conclusions: The pharmacological management of the lipid profile in these patients is important. A unique compound mutation in SMPD1 gene is described.