| 1 |  Murilo Antonio Fischer (BRA) | Garmin - Cervelo | 4:09:49 |
| 2 |  Oscar Freire Gomez (SPA) | Rabobank | s.t. |
| 3 | José Joaquin Rojas Gil (SPA) | Movistar | s.t. |
| 4 | Francisco José Ventoso Alberdi (SPA) | Movistar | s.t. |
| 5 |  Giacomo Nizzolo (ITA) | Leopard - Trek | s.t. |
| 6 |  Tony Gallopin (FRA) | Cofidis | s.t. |
| 7 | Dario Cataldo (ITA) | Quick Step | s.t. |
| 8 |  Klaas Lodewyck (BEL) | Omega Pharma - Lotto | s.t. |
| 9 |  Tom Leezer (NED) | Rabobank | s.t. |
| 10 |  John Degenkolb (GER) | HTC - High Road | s.t. |
| 11 | Johannes Fröhlinger (GER) | Skil - Shimano | s.t. |
| 12 | Sylvain Chavanel (FRA) | Quick Step | s.t. |
| 13 | Niki Terpstra (NED) | Quick Step | s.t. |
| 14 | Vicente Reynès Mimo (SPA) | Omega Pharma - Lotto | s.t. |
| 15 | Ruben Perez Moreno (SPA) | Euskaltel - Euskadi | s.t. |
| 16 |  Alexandr Kolobnev (RUS) | Team Katusha | s.t. |
| 17 | Fabian Wegmann (GER) | Leopard - Trek | s.t. |
| 18 | Philippe Gilbert (BEL) | Omega Pharma - Lotto | s.t. |
| 19 |  Ryder Hesjedal (CAN) | Garmin - Cervelo | s.t. |
| 20 | Gorka Izagirre Insausti (SPA) | Euskaltel - Euskadi | s.t. |
| 21 | Pello Bilbao López de Armentia (SPA) | Euskaltel - Euskadi | 0:00:05 |
| 22 | Amets Txurruka Ansola (SPA) | Euskaltel - Euskadi | s.t. |
| 23 |  Martin Velits (SVK) | HTC - High Road | s.t. |
| 24 | Eduard Vorganov (RUS) | Team Katusha | s.t. |
| 25 | Iban Velasco Murillo (SPA) | Euskaltel - Euskadi | s.t. |
| 26 | Vicente David Bernabéu Armengol (SPA) | Andalucia - Caja Granada | 0:00:07 |
| 27 | Bert Grabsch (GER) | HTC - High Road | s.t. |
| 28 | Jérôme Pineau (FRA) | Quick Step | s.t. |
| 29 | Bart De Clercq (BEL) | Omega Pharma - Lotto | s.t. |
| 30 | Luis León Sánchez Gil (SPA) | Rabobank | s.t. |
| 31 | José Vicente Toribio Alcolea (SPA) | Andalucia - Caja Granada | s.t. |
| 32 | Juan Jose Cobo Acebo (SPA) | Geox - TMC | s.t. |
| 33 | Luis Pasamontes Rodriguez (SPA) | Movistar | s.t. |
| 34 | Ion Izagirre Insausti (SPA) | Euskaltel - Euskadi | s.t. |
| 35 | Mikel Landa Meana (SPA) | Euskaltel - Euskadi | s.t. |
| 36 | Arkaitz Duran Aroca (SPA) | Geox - TMC | s.t. |
| 37 |  Matthias Brändle (AUT) | Geox - TMC | s.t. |
| 38 | Javier Ramirez Abeja (SPA) | Andalucia - Caja Granada | s.t. |
| 39 | Addy Engels (NED) | Quick Step | s.t. |
| 40 | Miguel Minguez Ayala (SPA) | Euskaltel - Euskadi | s.t. |
| 41 | Adrian Palomares Villaplana (SPA) | Andalucia - Caja Granada | s.t. |
| 42 | Haimar Zubeldia Aguirre (SPA) | Radio Shack | s.t. |
| 43 | José Herrada Lopez (SPA) | Caja Rural | s.t. |
| 44 | Markel Irizar Aranburu (SPA) | Radio Shack | s.t. |
| 45 |  Philip Deignan (IRL) | Radio Shack | s.t. |
| 46 | Nicolas Jonathan Castroviejo (SPA) | Euskaltel - Euskadi | s.t. |
| 47 | Sergio Mantecon Gutierrez (SPA) | Spain National Team | 0:00:20 |
| 48 | Sebastian Langeveld (NED) | Rabobank | 0:00:24 |
| 49 | Peter Velits (SVK) | HTC - High Road | 0:00:30 |
| 50 | David Blanco Rodriguez (SPA) | Geox - TMC | 0:00:31 |
| 51 | Denis Menchov (RUS) | Geox - TMC | 0:00:32 |
| 52 |  Fabio Andres Duarte Arevalo (COL) | Geox - TMC | s.t. |
| 53 | Linus Gerdemann (GER) | Leopard - Trek | 0:00:41 |
| 54 | Xavier Tondo Volpini (SPA) | Movistar | 0:00:48 |
| 55 | Beñat Intxausti Elorriaga (SPA) | Movistar | 0:00:57 |
| 56 |  Samuel Horstmann (SWI) | Price Your Bike | 0:01:02 |
| 57 |  Aleksejs Saramotins (LAT) | Cofidis | 0:01:14 |
| 58 | Pablo Urtasun Perez (SPA) | Euskaltel - Euskadi | 0:01:15 |
| 59 |  Christopher Jennings (RSA) | Burgos 2016 - Castilla y Leon | 0:03:13 |
| 60 | Carlos Verona Quintanilla (SPA) | Burgos 2016 - Castilla y Leon | s.t. |
| 61 | Oscar Grau Jorda (SPA) | Burgos 2016 - Castilla y Leon | s.t. |
| 62 | Víctor De La Parte Gonzalez (SPA) | Caja Rural | s.t. |
| 63 | Garikoitz Bravo Oiarbide (SPA) | Caja Rural | s.t. |
| 64 | Grischa Niermann (GER) | Rabobank | s.t. |
| 65 | Daniel Schorn (AUT) | Team Netapp | s.t. |
| 66 |  Steven Cozza (USA) | Team Netapp | s.t. |
| 67 | Inaki Isasi Flores (SPA) | Euskaltel - Euskadi | s.t. |
| 68 | Martijn Maaskant (NED) | Garmin - Cervelo | s.t. |
| 69 | Tyler Farrar (USA) | Garmin - Cervelo | s.t. |
| 70 | Aritz Etxebarria Etxebarria (SPA) | Orbea | s.t. |
| 71 | Danny Pate (USA) | HTC - High Road | s.t. |
| 72 | Mikel Bizkarra Etxeguibel (SPA) | Orbea | s.t. |
| 73 | Frederik Willems (BEL) | Omega Pharma - Lotto | 0:03:16 |
| 74 | Gert Dockx (BEL) | Omega Pharma - Lotto | s.t. |
| 75 |  Anders Lund (DEN) | Leopard - Trek | s.t. |
| 76 | Jon Aberasturi Izaga (SPA) | Orbea | 0:03:22 |
| 77 | Pablo Lechuga Rodriguez (SPA) | Andalucia - Caja Granada | s.t. |
| 78 | David Belda Garcia (SPA) | Burgos 2016 - Castilla y Leon | s.t. |
| 79 | Elias Schmäh (SWI) | Price Your Bike | s.t. |
| 80 | Patrick Schelling (SWI) | Price Your Bike | s.t. |
| 81 | Raul Alarcon Garcia (SPA) | Barbot - Efapel | s.t. |
| 82 | Aitor Galdos Alonso (SPA) | Caja Rural | 0:04:09 |
| 83 |  Oleg Chuzhda (UKR) | Caja Rural | s.t. |
| 84 | Guillaume Van Keirsbulck (BEL) | Quick Step | 0:06:27 |
| 85 | Julien Vermote (BEL) | Quick Step | s.t. |
| 86 | Vladimir Karpets (RUS) | Team Katusha | s.t. |
| 87 | Caleb Fairly (USA) | HTC - High Road | s.t. |
| 88 | Kevyn Ista (BEL) | Cofidis | s.t. |
| 89 | Brice Feillu (FRA) | Leopard - Trek | s.t. |
| 90 | Robert Wagner (GER) | Leopard - Trek | s.t. |
| 91 | Jesús Herrada Lopez (SPA) | Movistar | 0:08:09 |
| 92 |  Bruno Manuel Silva Pires (POR) | Leopard - Trek | s.t. |
| 93 | Kevin Seeldraeyers (BEL) | Quick Step | s.t. |
| 94 | Jens Voigt (GER) | Leopard - Trek | s.t. |
| 95 | Danilo Di Luca (ITA) | Team Katusha | 0:11:31 |
| 96 | Pablo Lastras Garcia (SPA) | Movistar | s.t. |
| 97 | Joan Sebastian Horrach Rippoll (SPA) | Team Katusha | s.t. |
| 98 | André Greipel (GER) | Omega Pharma - Lotto | s.t. |
| 99 | Diego Gallego Arnaiz (SPA) | Burgos 2016 - Castilla y Leon | 0:14:59 |
| 100 | Antonio Miguel Parra (SPA) | Spain National Team | s.t. |
| 101 | Lluís Guillermo Mas Bonet (SPA) | Burgos 2016 - Castilla y Leon | s.t. |
| 102 | Petr Ignatenko (RUS) | Team Katusha | s.t. |
| 103 | Diego Milán Jiménez (SPA) | Caja Rural | s.t. |
| 104 | Francisco Manuel Anton Marin (SPA) | Burgos 2016 - Castilla y Leon | s.t. |
| 105 | Jens Keukeleire (BEL) | Cofidis | 0:15:01 |
| 106 | Nico Sijmens (BEL) | Cofidis | s.t. |
