OBJECTIVE: This case report aims to: 1) Review a case of a dysmorphic child initially diagnosed as Hunters disease but eventually turned out to be Congenital Hypothyroidism. 2) Differentiate Hunters Disease from Congenital Hypothyroidism. 3) Discuss Congenital Hypothyroidism: it’s pathophysiology, clinical presentation, approach to diagnosis, treatment and prognosis. CASE SUMMARY: This is a case of a 13-year-old Filipino male who has been diagnosed as a case of Hunter Syndrome at 11 years old and was admitted at National Children’s Hospital due to chronic diarrhea of three weeks duration. He was initially managed as a case of Hypovolemic Shock secondary to Severe Dehydration, Chronic Diarrhea Secondary to Hunter’s syndrome. After the dehydration was corrected, it became apparent that he had other medical issues that needed attention. He was severely stunted with dysmorphic features and sluggish movements of the extremities. Skeletal survey revealed dystosis multiplex. Thyroid function tests confirmed the diagnosis of Congenital Hypothyroidism. CONCLUSION: This case just illustrated how misdiagnosis can lead to delayed treatment and well-being of the patient. The clinical features of this patient closely resemble both Hunter Syndrome and Congenital Hypothyroidism. So far, no existing link has been found to connect this metabolic syndrome with an endocrinologic pathology. Endocrinologic evaluation in children with Hunter Syndrome might be a gap in our medical knowledge that could be subject for further studies.