Sandhoff disease (SD) is a fatal, autosomal recessive lysosomal storage disease. Mutations in HEXB gene cause neuronal damage and SD due to accumulation of GM2 ganglioside. As ganglioside accumulates in the basal ganglia and white matter abnormalities occur, the T2 hypointensities of the basal ganglia, especially those of the thalamus, become observable on the magnetic resonance imaging (MRI). This is what leads to differential diagnosis. T2 hypointensities of the basal ganglia may be due to heterogeneous etiologies. Herein, we present an 18-month-old male patient who had progressive decline of motor functions, seizures, and bilateral thalamic hypointensity on T2-weighted MRI. Whole exome sequencing of the patient revealed homozygous c.1538T>C; p.Leu513Pro (RefSeq. NM_000521, GRCh38) HEXB mutation. Of note, our clinical findings were similar to those seen in patients with HEXB mutation. Exome sequencing allowed us to exclude genetic disorders with basal ganglia involvement.