Baldeschwieler has received multiple awards for his research, including the National Medal of Science, awarded in 2000, "For his imaginative development of new methods for determining the properties, structures, motions and interactions of molecules and molecular assemblies, the translation of these advances into practical pharmaceutical and instrumentation products for the public benefit, and extensive service to his government and the scientific community."[6] He was elected to the National Academy of Sciences in 1970, the American Academy of Arts and Sciences in 1972 and the American Philosophical Society in 1979.