Description Cliniface undertakes the visualisation, measurement, analysis, identification, and reporting of phenotypic traits from 3D facial images. These traits, known as Human Phenotype Ontology terms (or HPO terms), can then be used in concert with other phenotypic traits about a subject (e.g., behavoural or cognitive traits) to assist in diagnosing rare and genetic diseases. Cliniface works by fitting facial landmarks to the 3D model of a face and then taking spatial measurements using the landmarks to demarcate regions of interest. The extracted measurements are then compared to existing statistics from the research literature describing how these measurements are expected to change with age for different demographic cohorts. If measurements are found to fall outside of the expected range, this may indicate the presence of certain facial traits of clinical significance. Cliniface accepts 3D files in a variety of standard formats, and its analysis is saved into the 3DF file format which embeds metadata and analytic results as structured plain text alongside the original model data saved in Wavefront OBJ format. Analysis data can also be exported in XML and JSON formats to allow users to undertake further analysis outside of Cliniface.