Disclosed are methods and compositions for treating subjects with Cornelia de Lange Syndrome (CdLS). Specifically disclosed are methods for using Indomethacin or Acemetacin to treat subjects with CdLS. Also disclosed are methods for identifying compounds beneficial for the treatment of CdLS using an assay based on the expression of NIPBL or NIPBL homologous or orthologous genes. Also disclosed is a method of identifying compounds beneficial for the treatment of CdLS based on administering a test compound to Drosophila lava with reduced expression of Nipbl, and determining the normalization of CdLS phenotypes.