The 3q29 microdeletion syndrome (del 3q29) is a novel genomic disorder identified after the introduction of microarray-based technology. The phenotype of the reported patients is variable, including mental retardation and subtle facial anomalies. We report on two mother–daughter pairs, heterozygous for 3q29, and review clinical features of all known affected individuals. Del 3q29 syndrome is associated with nonspecific clinical features, including mild-to-moderate developmental delay, microcephaly, and mild facial dysmorphisms such as short philtrum and high nasal bridge. Facial anomalies were nonoverlapping and nondistinct, also within each mother–daughter pair. Parental transmission of del 3q29 could be more frequent than previously considered. Malformations are rare, occurring only in single subjects. The phenotypic diversity of affected patients and the lack of distinct dysmorphisms suggest that this disorder cannot be recognized on clinical ground alone. Del 3q29 should be searched in subjects with unexplained mild/moderate mental retardation, microcephaly, and minor nonspecific facial anomalies. © 2009 Wiley-Liss, Inc.