Stage 1: Frederikshavn–Viborg, Denmark (210 km)

The 2006 Danmark Rundt started in Frederikshavn and the first stage took the riders across Vendsyssel before turning south towards Viborg. This was also the race's longest stage.

Route: Frederikshavn–Hjørring–Løkken–Brovst–Løgstør–Farsø–Gedsted–Skals–Viborg, ending with 2 laps of 4.5 km.

Results

#	Rider	Team	Time
1	Aitor Galdos Alonso	Panaria Navigare	4h44'08"
2	René Haselbacher	Gerolsteiner	s.t.
3	Stuart O'Grady	Team CSC	s.t.
4	Manuel Quinziato	Liquigas–Bianchi	at 10"
5	Maximiliano Richeze	Panaria Navigare	at 18"
Full result

This meant that Aitor Galos Alonso lead the general classification, as well as the point classification. Aart Vierhouten lead the hill competition, Alex Rasmussen held the youth jersey, Jacob Nielsen the fighter jersey and Gerolsteiner lead the team competition.

Stage 2: Aalestrup–Vejle (185 km)

Stage 2 took the riders south through Jutland, reaching the race's highest point some 170 metres above sea level at Yding Skovhøj. The stage also featured a rough 21% climb on Kiddesvej in Vejle which was included on both of the final laps.

Route: Aalestrup–Møldrup–Viborg–Dollerup Bakker–Kjellerup–Silkeborg–Gl. Rye–Yding Skovhøj–Uldum–Vejle, ending with 2 laps of 5.5 km.

Results

#	Rider	Team	Time
1	Fabian Cancellara	Team CSC	4h16'34"
2	Stuart O'Grady	Team CSC	at 21"
3	Thomas Ziegler	Team T-Mobile	s.t.
4	Cadel Evans	Davitamon–Lotto	at 23"
5	Baden Cooke	Unibet.com Cycling Team	s.t.
Full result

This means that Fabian Cancellara moved into yellow and took the white youth-jersey too, although Aitor Galdos Alonso retained the dark-purple point-jersey. Aart Vierhouten kept the dotted hill-jersey, and Maarten Tjallingi took the fighter-jersey. Team CSC moved into first in the team classification.

Stage 3: Kolding–Odense (205 km)

The third stage reached the Little Belt Bridge before following the western and south coast of Funen until Svendborg, then heading north to the island's largest city, Odense.

Route: Kolding–Middelfart–Assens–Hårby–Faaborg–Svendborg–Ringe–Odense, ending with 2 laps of 4.4 km.

Results

#	Rider	Team	Time
1	Robert Förster	Gerolsteiner	4h40'41"
2	Stuart O'Grady	Team CSC	s.t.
3	Alex Rasmussen	Team Post Danmark	s.t.
4	Aart Vierhouten	Skil–Shimano	s.t.
5	Maximiliano Richeze	Panaria Navigare	s.t.
Full result

After stage 3, Stuart O'Grady held the yellow and purple jerseys. Aart Vierhouten kept the dotted jersey, and Fabian Cancellara was still the best youngster. Jacob Nielsen took the fighter jersey, and Team CSC was still on top of the team-leaderboard.

Stage 4: Sorø–Hillerød (100 km)

Stage 4 was a so-called "half-stage", with an individual time trial being held in the evening of 5 August. The stage went north-east from Sorø through Tølløse, birth city of 2005 and 2006 Tour de France polka-dot winner Michael Rasmussen, on its way to Hillerød.

Route: Sorø–Stenlille–Tølløse–Kirke Hyllinge–Skibby–Frederikssund–Slangerup–Hillerød, ending with 2 laps of 4.0 km.

Results

#	Rider	Team	Time
1	Olaf Pollack	T-Mobile Team	2h30'04"
2	Baden Cooke	Unibet.com Cycling Team	s.t.
3	Stuart O'Grady	Team CSC	s.t.
4	René Haselbacher	Gerolsteiner	s.t.
5	Dariusz Rudnicki	Team Intel Action	s.t.
Full result

No classements got new leaders in this short stage, leaving O'Grady leading the individual classification and CSC the team classification.

Stage 5: Elsinore (14 km, ITT)

Stage 5, the penultimate stage, was a short individual time trial. A few days before this stage, it was shortened from 15.5 to 14 km. The stage took place on the same day as stage 4.

Route (streets are unlinked): Kronborgvej–Ndr. Strandvej–Hellebæk–Ålsgårde (turning point)–Hellebæk–Elsinore–Kronborgvej

Results

#	Rider	Team	Time
1	Fabian Cancellara	Team CSC	0h16'15"
2	Thomas Ziegler	Team T-Mobile	at 18"
3	Alex Rasmussen	Team Post Danmark	at 24"
4	Vincenzo Nibali	Liquigas–Bianchi	at 27"
5	Stuart O'Grady	Team CSC	at 27"
Full result

Stage 6: Gilleleje–Frederiksberg (156 km)

The final stage crossed Benbrækkeren, a steep hill in northern Zealand, before ending with the traditional finish at Frederiksberg Allé.

Route: Gilleleje–"Benbrækkeren"–Helsinge–Hillerød–Blovstrød–Vedbæk–Frederiksberg, ending with 10 laps of 6.0 km.

• Stage winner: Robert Förster