In the late 1999, a new, larger "second generation" Odyssey appeared in Japan and Australia and as a Left hand Drive (LHD) in China. However, this new Odyssey was a major upgrade of the first generation Odyssey rather than a completely new model. As a result, its overall shape and appearance were similar to the first generation Odyssey. Still, it was 85 mm (3.3 in) longer and 10 mm (0.4 in) wider than the previous model; while the saloon's length was shortened. The base model continued to be sold with a 2.3 L 4-cylinder engine F23A RA6(2WD) & RA7(4WD), however, the a 3.0 L VTEC V6 engine J30A (from the first generation, producing now 210 hp (157 kW)) was available with RA8(2WD) & RA9(4WD). The 2000 Odyssey was the first Honda to receive a 5-speed automatic transmission (with the 3.0L engine). All the second generation gearboxes also featured another first – a tiptronic-like manual mode, known as "Honda S-matic", in which a gearbox remains to be a classic Honda's hydro-automat, but the driver is able to manage the shifting moment (if electronically allowed) with the selector's '+' & '-' positions.
The interior was completely new. The old automatic column shifter was moved to the centre console. Digital climate controls replaced the old manual controls, and were situated near the audio system controls. Woodgrain trim was standard on all models, while in V6-L models leather was standard. The interior configuration was also changed (second and third row), and the spare wheel was moved to a new position beneath the third row. With L and Absolute versions, an additional third-row heater was added. The sunroof was no longer available.
A sporty 'Absolute' version with all the chassis for the first time has appeared. This co-Mugen tuned version differs by the modified suspension of the European-like car's behavior, 17-inch wheels and some exterior/interior changes.
In January 2003, the Odyssey was given a mild restyle. It received new, larger Honda emblems for the front and rear, clear-lens tail-lights (replacing amber), and a larger front grille with 4 chrome strips instead of 3. Pricing was reduced by US$2,000 (US$24,490) for the 4-cylinder, and US$4,000 for the V6 (US$30,490). In the Australian market, the new Odyssey proved more popular than its predecessor, at least initially. However, in 2002, sales hit an all-time low, and in 2003, sales of only 649 units were almost one-third of the total in 2000.