The Lick Branch: The Lick Branch left the Southern Pacific (now Union Pacific) Coast Line a few miles south of San Jose, at a location called Lick. The branch proceeded for a few miles, generally southwest, to its original end at the QuickSilver mines at New Almaden. Along the route, the line served orchards, gravel pits, Hubbard and Johnson Lumber and the Almaden Winery.

The line was shortened due to an abandonment of the section south of Alamitos in 1937. The remainder was formally abandoned in January of 1981, but the last train most likely ran in 1979.

Most of the right-of-way cannot be traced easily, as there are now housing subdivisions along much of its route. Not far from the main line junction, the right of way is used for a self storage facility. Further south, the last couple miles of the branch ROW are now used for the VTA light rail system, built in the early 1990s. The single track light rail line includes the Oakridge and Almaden stations on the former SP segment.

The San Jose Branch: The Western Pacific reached Oakland in the early 1900s after the other rail lines in the area were already established. A branch from Niles to San Jose was completed in 1921, and is the southernmost part of the WP. A map of the branch shows it was shaped like a "J", with the hook curving around the south and west sides of San Jose. (See also Niles to Milpitas.)

It crossed the SP main and a few SP branches along its route. The WP was absorbed by the UP in 1982, but it wasn't until the SP was also merged into the UP (1996) that the last few miles of the branch were abandoned. Several connecting industrial spurs have also been pulled up recently.

As of fall 2003 the tracks are "out of service" between William Street Yard (east side of San Jose) through Valbrick (former SP spur crossing) to the former SP coast line crossing (CP Michael). Beyond that location, through West San Jose (SP Permanente branch crossing) to the end of the branch, most of the rails and ties were removed in 2003. Some rails remain at grade crossings, but the signals are removed or have "Tracks Removed From Service" signs on them. In a couple of places near West San Jose, buildings are under construction on the former right-of-way. Meanwhile, a small section near the end of the branch, used for a customer, has been connected to the UP/SP Permanente Branch. (As of late 2003 the Permanante branch was being double tracked for use as a future light rail line, while still maintaining freight service).

The 4th Street Line: This line was once part of the Southern Pacific's main line through San Jose, CA, the Coast Line. While the mainline was relocated to where it is today, this line remained as a branch of the mainline; it was called the 4th Street Line, since part of it ran in the pavement of its namesake street.

Today, most of the line is abandoned, except for a small central portion of it, used to connect to the Luther Industrial Spur, still in use by Union Pacific.

See also the The Colma Branch.

The 7th Street Spurs: This maze of spurs along 7th street in San Jose, CA, was used by the Western Pacific and Southern Pacific, and branch off of the San Jose Branch and the 4th Street Line, respectively.

The spurs fell into disuse over the past two decades and Union Pacific pulled up what was left of the tracks in early 2008.