Judith Butler, a respected American leftist feminist intellectual who teaches at Berkeley was honoured at the parade, but used her moment in front of the microphone to reject the prize and criticise the march.
Renate Künast, head of the Green Party, first praised Butler for her work before the 54-year-old professor took to the stage at the Brandenburg Gate.
But rather than accepting the prize, she rejected it, saying the parade had become too commercial, and was ignoring the problems of racism and the double discrimination suffered by homosexual or transsexual migrants.
Reading in German from a paper, she said an alternative Christopher Street Day, which is organised in the Kreuzberg area of the city and due to be held next Saturday, was much more effective at tackling such questions.
Around 600,000 people are estimated to have attended the parade which included around 50 trucks and groups of costumed marchers and dancers.