We observed a neonate who had severe thrombocytopenia wherein evaluations for neonatal immune-mediated thrombocytopenia and congenital infections were negative, and the marrow findings were consistent with congenital amegakaryocytic thrombocytopenia (CAMT). A genomic microarray identified a microdeletion at 21q22.11 including the gene RUNX1. Two somewhat similar cases were recently reported, but with multiple congenital anomalies that are not present in our case. We propose that a 21q22 deletion resulting in RUNX1 haploinsufficiency can produce a phenotype similar to CAMT with various associated anomalies depending on which adjacent genes are absent or disrupted.