With his Ph.D. student Benno Müller-Hill, Gilbert was the first to purify the lac repressor, just beating out Mark Ptashne for purifying the first gene regulatory protein.

The Gilbert-Maxam method for sequencing DNA. In 1980 Gilbert shared the 1980 Nobel Prize in Chemistry with Frederick Sanger and Paul Berg. Berg received half of the prize "for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA". The other half was split between Gilbert and Frederick Sanger "for their contributions concerning the determination of base sequences in nucleic acids". This paper is available from PNAS at this link.