Background Hypophosphatasia (HPP) is a rare inherited disorder affecting bone and teeth development. Perinatal HPP is the most severe form and associated with a high mortality. Features include respiratory distress, skeletal abnormalities and low alkaline phosphatase (ALP) activity.

Case A baby boy developed respiratory distress, hypotonia and seizures within an hour of birth. Blood gas showed mixed acidosis and abnormal base deficit. Hypoxic–ischaemic encephalopathy (HIE) was suspected and managed with therapeutic hypothermia. Subsequent investigations identified low ALP activity and abnormal bone mineralisation, leading to a diagnosis of HPP. On day 5 of life, enzyme replacement therapy (ERT) was commenced, its first use via direct NHS England funding since UK licensing in 2017.

Conclusions Early hypotonia is an atypical presentation for perinatal HPP. Combined with acidosis and encephalopathy, it can clinically mimic HIE. Early recognition of biochemical and radiological features of HPP is essential for rapid diagnosis and timely initiation of life-saving ERT.