The Honda CBR1000RR was the successor to the CBR954RR. While evolving the CBR954RR design, few parts were carried over to the CBR1000RR. The compact 998 cc (60.9 cu in) in-line four was a new design, with different bore and stroke dimensions, race-inspired cassette-type six-speed gearbox, all-new ECU-controlled ram-air system, dual-stage fuel injection, and center-up exhaust featuring a new computer-controlled butterfly valve. The chassis was likewise all new, including an organic-style aluminum frame composed of Gravity Die-Cast main sections and Fine Die-Cast steering head structure, inverted fork, Unit Pro-Link rear suspension, radial-mounted front brakes, and a centrally located fuel tank hidden under a faux cover. Additionally, the Honda Electronic Steering Damper (HESD) debuted as an industry first system which aimed to improve stability and help eliminate head shake while automatically adjusting for high and low speed steering effort.
A longer swingarm acted as a longer lever arm in the rear suspension for superior traction under acceleration and more progressive suspension action. Longer than the corresponding unit on the CBR954RR (585 mm (23.0 in) compared to 551 mm (21.7 in)) the CBR1000RR's 34 mm (1.3 in) longer swingarm made up 41.6 percent of its total wheelbase. The CBR1000RR's wheelbase also increased, measuring 1,405 mm (55.3 in) a 5 mm (0.20 in) increase over the 954.
Accommodating the longer swingarm was another reason the CBR1000RR power plant shared nothing with the 954. Shortening the engine compared to the 954 meant rejecting the conventional in-line layout. Instead, engineers positioned the CBR1000RR's crankshaft, main shaft and countershaft in a triangulated configuration, with the countershaft located below the main shaft, dramatically shortening the engine front to back, and moving the swingarm pivot closer to the crankshaft. This configuration was first successfully introduced by Yamaha with the YZF-R1 model in 1998 and inspired superbike design in the following years.
Positioning this compact engine farther forward in the chassis also increased front-end weight bias, an effective method of making high-powered liter bikes less wheelie prone under hard acceleration. This approach, however, also provided very little space between the engine and front wheel for a large radiator. Engineers solved this problem by giving the RR a modest cylinder incline of 28 degrees, and moving the oil filter from its frontal placement on the 954 to the right side of the 1000RR engine. This allowed the RR's center-up exhaust system to tuck closely to the engine.