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Chronic intestinal pseudoobstruction (CIPO) is a severe form of intestinal dysmotility, and patients often undergo iterative abdominal surgeries and require parenteral nutrition. Several genes are known to be responsible for this pathology, including ACTG2 (autosomal dominant) and MYH11 (autosomal recessive).We report the first case of unexpected trio medical exome sequencing diagnosis of mucopolysaccharidosis type I (MPS-I) in a patient with an early CIPO. There was no clinical suspicion of MPS-I at the time of the prescription. It allowed biochemical confirmation of MPS-I, expert clinical evaluation and early treatment. Enzyme replacement therapy (ERT) with laronidase was started at 9 months old, and hematopoietic stem cell transplantation was carried out at 10 months and a half. The patient also had a 1.7 mb heterozygous deletion in chromosomal region 16p13.11p12.3, comprising several genes, including MYH11, paternally inherited. Her father has no symptoms of CIPO or other digestive symptoms. One previous association of CIPO and MPS-I was reported in 1986. Moreover, the number of incidental findings of inherited metabolic disorders with therapeutic impact will inevitably increase as pangenomic analyses become cheaper and easily available.