Saethre-Chotzen syndrome (SCS) is a craniosynostosis syndrome characterized by facial and limb abnormalities caused by mutations in the TWIST1 gene on 7p21, resulting in variable loss of function. The transcription factor TWIST1 has also been shown to promote tumor growth and has been linked to the formation of metastases in breast cancers. One suggestive case of inherited SCS and malignancy in childhood has been reported previously. Here, we present immunological and genetic investigations including the determination of a new stop codon mutation in the TWIST1 gene in SCS associated with malignancy in childhood.