The Refugee Health Information System (RHIS) for humanitarian settings was developed by the United Nations High Commissioner for Refugees (UNHCR) in 2004. As of 2009, it contained seven categories related to mental, neurological and substance use (MNS) conditions: epilepsy/seizure, alcohol/substance use disorder, mental retardation/intellectual disability, psychotic disorder, severe emotional disorder, medically unexplained somatic complaint and other psychological complaint. During a recent overhaul of the RHIS, the MNS categories were revisited. This article describes the revision process and provides insights into how and why changes were made. Two rounds of consultations involving 34 expert reviewers in humanitarian mental health led to nine case definitions for MNS conditions in the new integrated RHIS (iRHIS): epilepsy/seizure, alcohol/substance use disorder; intellectual disability/developmental disorder; psychotic disorder (including mania); delirium/dementia; depression or other emotional disorder; other emotional complaint; medically unexplained somatic complaint; and self-harm/suicide. The use of additional specifiers enables dedicated mental health professionals in humanitarian settings to document a more refined diagnosis with a total of 22 different categories that made the system compatible with the modules of the Mental Health Gap Action Programme, without additional complexity.