The New South Wales state-wide newborn screening programme has offered comprehensive screening for inborn errors of metabolism, including MSUD, using electrospray tandem mass spectrometry since 1998. Over this period, a number of patients with classic MSUD have been identified with subsequent good neurological outcome. We describe two patients with an intermediate form of MSUD who presented later in childhood. Retrospective review of their newborn screening results demonstrates that the diagnosis could not have been made by current newborn screening. Their neurological outcome is much less satisfactory. Despite the usefulness of expanded newborn screening programmes in detecting severe neonatal presentations of inborn errors of metabolism, partial enzyme deficiencies may not be detected. Metabolic diseases still need to be considered in appropriate clinical situations later in life.