Students, dons and members of the public gathered outside Balliol College in the centre of the city for a march close to the site of the 18m biomedical research laboratory being built in Oxford.
The construction project was thrown into limbo in 2004 after the original building contractor pulled out, amid growing protests from animal rights activists and suggestions of intimidation by extremists.
After a 17-month break, the project finally got back underway late last year, by which time the controversy had escalated, with arson attacks on two sports buildings owned by Oxford colleges.
Before the march set off, Prof John Stein an Oxford University professor of physiology, told the crowd: "This is a historic day. We are drawing a line in the sand."
In a reference to Oxford's past medical breakthroughs, Prof Stein said: "Imagine yourself a mother with a three-year-old with meningitis.
"Fifty years ago, that child would have died. Now, due to the discovery and isolation of penicillin in this university, we can stop that child dying.
"Do we stop her getting penicillin just because it had been tested on 20 rats?" The crowd shouted: "No."
Local MP, Dr Evan Harris, who is also the Liberal Democrat spokesman for science, told the crowd that he had acted as a human guinea pig in tests for HIV and Aids treatments.
Dr Harris received cheers from the crowd as he said: "My message to the extremists is that you will never win."
As the march got close to the site of the laboratory, the pro-research demonstrators were held back behind police lines, around 200 yards away from a smaller but boisterous demonstration by animal rights campaigners.