Patients with inborn errors of metabolism and their families require unique clinical care including management of acute illnesses, screening for long term complications, discussion of the etiology of the condition, connections to social supports, and clarification of the recurrence risks and prenatal testing and treatment options. Our multidisciplinary pediatric metabolic clinic combines the skills of metabolic geneticists, pediatric dieticians, social workers, clinical pharmacists, nurses and genetic counselors to provide optimal and well-rounded care for our patients and their families. Given the inherited nature of most inborn errors of metabolism and the necessary long-term management for these disorders, the genetic counselor's role in this clinic setting is integral in providing ongoing support and education for patients and their families. This includes coping with the disease burden, helping patients and families adapt to a condition in the family and ensuring adequate understanding of the genetic risks and the available prenatal diagnostic and reproductive choices. Our clinic provides services to a large geographic area with many isolated populations where unique metabolic diseases are highly prevalent secondary to a founder effect. In this paper, we share our experience in providing longitudinal care to children with complex medical needs due to metabolic disorders and highlight the role of the genetic counselor in this clinic setting.