Riding in front of home fans, the Swiss rider enjoyed plenty of support from the roadside, and duly delivered with his fifth win of the season.
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He posted a time just one second quicker than Jurgen Roelandts (Lotto-Soudal), who was for a while the surprise rider in the hot-seat ahead of more recognised prologue specialists. Orica GreenEdge’s Luke Durbridge was third.
Geraint Thomas (Sky) had been a pre-race favourite, but didn’t have one of his best days and finished outside of the top ten in 14th, 12 seconds down.
He joins several other riders with aspirations of winning the overall GC who also finished outside the top ten, including Tejay van Garderen (BMC), Rui Costa (Lampre-Merida), Robert Gesink (LottoNL-Jumbo) and defending champion Simon Spilak (Katusha).
The 6.4km course through Baar was technical with plenty of sharp turns. Alex Dowsett (Movistar) crashed on one particularly tight corner, ending his hopes for a high placing after being one of the quickest through the intermediate time check. The British time-trial champion crossed the line way down in the standings in 172nd place, battered and bruised with several rips in his skin suit.
The course would have been more treacherous had the dark clouds that gathered produced more rainfall, but conditions generally remained dry and only the last few riders had to ride through some light drizzle.
There was some panic when the one kilometre to go inflatable banner collapsed, but no rider appeared to be affected.
Sunday’s second stage sees the riders take on a route from Baar to Baar over 187.6km.
Tour de Suisse 2016, stage one, Baar – Baar, 6.4km (and overall standings)
1 Fabian Cancellara (Swi) Trek-Segafredo in 7-38
2 Jürgen Roelandts (Bel) Lotto Soudal at 1s
3 Luke Durbridge (Aus) Orica-GreenEdge at 2s
4 Martin Elmiger (Swi) IAM Cycling at 6s
5 Jon Izagirre Insausti (Esp) Movistar Team at s.t
6 Tim Wellens (Bel) Lotto Soudal at 7s
7 Johan Le Bon (Fra) FDJ at 9s
8 Silvan Dillier (Swi) BMC Racing Team at s.t
9 Gorka Izagirre Insausti (Spa) Movistar Team at 10s
10 Wilco Kelderman (Ned) Team LottoNl-Jumbo at s.t.
14. Geraint Thomas (GBr) Team Sky, at 12s