The Trek Madone 5.9 is different from the 5.2 and 5.5 models in that the drivetrain combines Shimano Ultegra and Shimano Dura-Ace parts to strike a new balance and get the best of both worlds. The brakeset returns to the Shimano Ultegra parts for this model.
The Trek Madone 5 series all feature Bontrager Race X Lite forks and tires, with Bontrager Race Lite wheels. The saddle is Bontrager inForm Race Lite on a carbon seatmast cap, and the handlebars are Bontrager Blade VR on a Bontrager Race X Lite stem. Note that the Trek Madone 5.9 is the only bike in the entire Madone line that doesn't have a WSD model.