Chromosomal deletion including 5q31 is rare and only a few patients have been reported to date. We report here on the first two patients with a submicroscopic deletion of 5q31.3 identified by microarray-based comparative genomic hybridization. The common clinical features of both patients were marked hypotonia, feeding difficulty in infancy, severe developmental delay, and epileptic/nonepileptic encephalopathy associated with delayed myelination. Both patients also shared characteristic facial features, including narrow forehead, low-set and abnormal auricles, bilateral ptosis, anteverted nares, long philtrum, tented upper vermilion, edematous cheeks, and high palate. The deleted region contains clustered PCDHs, including PCDHA and PCDHG, which are highly expressed in the brain where they function to guide neurons during brain development, neuronal differentiation, and synaptogenesis. The common deletion also contains neuregulin 2 (NRG2), a major gene for neurodevelopment. We suggest that 5q31.3 deletion is responsible for severe brain developmental delay and distinctive facial features, and that the common findings in these two patients representing a new microdeletion syndrome. We need further investigations to determine which genes are responsible for the patients' characteristic features. © 2011 Wiley-Liss, Inc.