Hypoparathyroidism is a rare disorder which is predominantly of idiopathic or genetic origin in children. The diagnosis is made from the biochemical measurement of parathyroid hormone (PTH), and the key findings include a low PTH in combination with hypocalcemia and hyperphosphatemia. However, the level of PTH encountered in patients with hypoparathyroidism may be dependent on the underlying genetic cause of the disorder as well as the biochemical assay used for assessment of PTH. A three-year-old child with asymptomatic primary hypoparathyroidism was identified with a homozygous missense variant of PTH. A sudden unexpected high PTH result after a shift from 2nd to 3rd generation PTH assay in the routine laboratory provided a clue on the underlying genetic etiology. Pathogenic variants of PTH as a cause of hypoparathyroidism are rarely described. In this case, the child was asymptomatic, and discordant PTH results were seen with different assays.