Microtia was found in a transgenic mouse 643 and all offspring with microtia had the transgene. No anomalies, other than occasional low set ear and abnormal biting, were identified in other tissues and organs. In the developmental analysis, on the 9th and 10th days of gestation, hypoplasia of the second branchial arch was observed, while various kinds of malformed hillocks were noted on the 12th day. All of these anomalous embryos were transgenic. Histologically, hemorrhage and subsequent phagocytosis were noted at the second branchial arch. Left sided anomalies were predominant and in bilaterally defective ones asymmetry existed. These findings closely resembled to those in experimental animals with a phenocopy of the first and second branchial arch syndrome in humans. Since all other transgenic mouse lines with the same transgene as 643 appeared normal, this dysmorphic phenotype may be caused by an insertional mutation of a host gene, although inappropriate expression of the transgene should be examined further as a possible cause. These results suggest that this transgenic mouse line 643 may be useful as an animal model of branchial arch anomalies in humans.