The 55-year-old Irishman has been the 'president elect' for two years but recent months have seen bitter infighting from those opposed to Verbruggen's favoured successor.
Darsan Singh of Malaysia withdrew his candidacy before the vote went ahead. There's no indication on the UCI's website whether the election of its president is conducted by secret ballot.
The Spanish cycling federation tried to get a Swiss court to prevent Hein Verbruggen from overseeing today's vote. However, on Wednesday the legal action was thrown out.
Last week, French newspaper L'Equipe reported a claim that the UCI influenced the vote for president of the African cycle federations. The Algerian candidate said the UCI had moved the election from Africa to Rome, with all expenses paid. It was claimed there were cash bribes, too.
The Egyptian candidate won and he was believed to be Verbruggen's favoured candidate.
McQuaid may have won today's vote but his new post could be a poisoned chalice, with further legal challenges likely.
Considered less confrontational than Verbruggen, McQuaid will have to spend much of his time closing the rifts that have developed in cycling in the past few months.