He replaces Olusegun Obasanjo, who plucked him from relative obscurity as a quiet northern state governor to be his successor.
And that has raised questions as to just how independent the new leader can be, given how much he owes to the old guard.
Mr Obasanjo is not making it easy - he will remain head of the governing People's Democratic Party.
And in his last few weeks in power, Mr Obasanjo has sold off a large number of state assets to his allies in the private sector.
Still, this inauguration is a unique occasion in a country whose history is littered with coups and military rule.
But the handover is marred by the fact that Mr Yar'Adua comes to office on the back of deeply flawed elections. 
They were condemned by observers both at home and abroad as simply "not credible".
Overcoming the issue of legitimacy is just one of the tasks facing Mr Yar'Adua.
He has now got to rule Africa's most populous nation, whose sheer size and resources make it of real strategic importance.
It is the continent's major oil producer but is riven by corruption and insecurity.
Most people lack even the most basic amenities, such as running water and electricity and they live in poverty despite the government receiving billions of dollars in oil revenues.
Turning all that around will not be easy.
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