In 1969, Gilbert was awarded Harvard's Ledlie Prize. In 1972 he was named American Cancer Society Professor of Molecular Biology. In 1979, Gilbert was awarded the Louisa Gross Horwitz Prize from Columbia University together with Frederick Sanger.[3][23] That year he was also awarded the Gairdner Prize and the Albert Lasker Award for Basic Medical Research.
Gilbert was awarded the 1980 Nobel Prize in Chemistry, shared with Frederick Sanger and Paul Berg. Gilbert and Sanger were recognized for their pioneering work in devising methods for determining the sequence of nucleotides in a nucleic acid.
Gilbert has also been honored by the National Academy of Sciences (US Steel Foundation Award, 1968); Massachusetts General Hospital (Warren Triennial Prize, 1977);[citation needed] the New York Academy of Sciences; (Louis and Bert Freedman Foundation Award, 1977), the Académie des Sciences of France (Prix Charles-Leopold Mayer Award, 1977). Gilbert was elected a Foreign Member of the Royal Society (ForMemRS) in 1987.
In 2002, he received the Biotechnology Heritage Award, from the Biotechnology Industry Organization (BIO) and the Chemical Heritage Foundation.
Allan Maxam and Walter Gilbert's 1977 paper "A new method for sequencing DNA" was honored by a Citation for Chemical Breakthrough Award from the Division of History of Chemistry of the American Chemical Society for 2017. It was presented to the Department of Molecular & Cellular Biology, Harvard University.