Phase I, about 520 miles (840 km) long using high-speed rail through the Central Valley, will connect San Francisco to Los Angeles.

In Phase 2, the route will be extended in the Central Valley north to Sacramento, and from east through the Inland Empire and then south to San Diego.

The 2022 Business Plan[9] focuses on developing an Interim Initial Operating Segment (IOS) between Merced and Bakersfield.

Although the Authority is focused on getting the Interim IOS in the Central Valley in operation by the end of the decade, it is also looking ahead to the next step (that is, connecting to San Francisco using the prepared Caltrain blended route).

[10] East of Gilroy the alignment becomes a pure HSR section with approximately 15 miles (24 km) of tunnels through the Pacheco Pass.

When tunnel field studies, early engineering, and design work are completed for this section, it will be ready for construction when funding is available.

[13] Both the high-speed trains and the new Caltrain EMUs will be able to run at 110 mph (180 km/h) on shared tracks from San Jose north.

Service is planned to be extended to the Salesforce Transit Center once the Downtown Rail Extension (now known as The Portal) is completed.

[15] The Authority recognizes the value of adding this link as soon as possible to the Initial Operating Segment (IOS), and is exploring ways of obtaining additional funding for it.

[16] South of San Jose, CHSR will continue to share the Union Pacific right-of-way until it reaches Gilroy, when it will switch onto dedicated HSR tracks for the remainder of the route to Merced.

[18] The Pacheco Pass alignment going through the Grasslands Ecological Area has been criticized by two environmental groups, The Sierra Club and the Natural Resources Defense Council.

[19] A coalition that includes the cities of Menlo Park, Atherton, and Palo Alto has also sued the Authority to reconsider the Altamont Pass alternative.

The Authority plans conventional rail upgrades for the Altamont corridor, to complement the high-speed project.

East of Gilroy the alignment becomes a pure HSR route with approximately 15 miles (24 km) of tunnels through the Pacheco Pass.

When tunnel field studies, early engineering, and design work are completed for this section, it will be ready for construction when funding is available.

California High-Speed Rail trains will use the structure to switch between the three branches of the Phase I system: westward towards the San Francisco Peninsula, southward towards Bakersfield (and later southern California), and northwards towards Merced (where passengers may transfer to other rail services until the line is extended to Sacramento).

[28] In 2019 the California High-Speed Rail Authority selected the final alignment: the State Route 152 / Road 11 option.

[29] The entire 60-mile (97 km) segment from Merced to Fresno in the Central Valley will run on dedicated HSR tracks.

[30] The southern portion of this segment (north of Madera to Fresno) has received route approval and is undergoing construction.

[31] The 114-mile (183 km) segment in the Central Valley will run on dedicated HSR tracks for the Initial Operating Section in 2029.

[41] The 33 miles (53 km) from Los Angeles to Anaheim will run on an upgraded Metrolink corridor for Phase 1 Blended in 2033.

Note: The Authority considered a mid-peninsula station in Redwood City, Mountain View, or Palo Alto, but it was removed from the business plan in May 2016 due to low ridership projections, although the possibility was raised of adding one in the future.

[49] The southernmost segment from Los Angeles to San Diego will be built on dedicated high-speed rail tracks with several routing and stations options.

Key stations are identified as:[50] Trains may additionally call at: San Diego is considering how high-speed rail can play a role in their transportation options as Lindbergh Field is expected to reach maximum capacity between 2025 and 2030.

Airport consultant suggest that the train could provide an alternative for California destinations such as Los Angeles, San Francisco, Sacramento and Ontario.