His campaign was conducted as an independent write-in candidate, because he waited to declare his candidacy until September, after the ballots had already been printed. Three days before the election, the Kansas attorney general (who had prosecuted Brinkley before the medical board) announced that the rules surrounding write-in candidates had changed, and that the doctor's name could only be written in one specific way for the vote to count (as J. R. Brinkley). As a write-in candidate, he received more than 180,000 votes (29.5 percent of the vote) and lost to Harry Hines Woodring, later Secretary of War in the cabinet of President Franklin D. Roosevelt. An article published at the time in "The Des Moines Register" estimated that between 30,000 and 50,000 ballots were disqualified in this manner. Woodring later admitted that had those votes counted, Brinkley would have won.