Hereditary hypomagnesemia with secondary hypocalcemia (HSH) is a rare condition caused by mutations in the transient receptor potential melastatin 6 (TRPM6) gene. Patients usually present during early infancy with symptomatic hypocalcemia; however, intracranial calcification has not been previously reported in HSH. We report on a three-month-old Saudi girl who presented with hypocalcemic convulsions and was initially treated as nutritional rickets. However, further biochemical analysis of blood and urine were suggestive of HSH. This diagnosis was confirmed by mutation analysis, which identified a novel homozygous frame shift mutation (ins 2999T) of the TRPM6 gene. A computed tomography brain scan, done around the time of diagnosis, identified bilateral basal ganglia calcification (BGC). Her serum calcium and the BGC improved with magnesium replacement. BGC can be added as a new feature of HSH and the case highlights the importance of measuring serum Mg in patients with hypocalcemic convulsions, particularly in children of consanguineous parents.