List of former Long Island Rail Road lines

The North Shore Freight Branch ran from the Main Line at Sunnyside Yard west to the East River where Gantry Plaza State Park is now.

The Evergreen Branch connected the Bushwick Branch east of Bushwick Terminal with the Bay Ridge Branch north of East New York.

The Manhattan Beach Branch ran south from the Bay Ridge Branch at Flatbush to Manhattan Beach.

The Whitestone Branch split from the Port Washington Branch near Flushing and ran north and east to Whitestone.

The Woodside Branch ran north of the current Port Washington Branch between Woodside and the Whitestone Branch west of the Flushing River.

The Flushing Branch was a short spur southeast from the Port Washington Branch in Flushing.

The Cedarhurst Cut-off was an extension of the Montauk Branch from its merger with the Atlantic Branch at Springfield Junction to the Cedarhurst, where it would turn west and run parallel to the Far Rockaway Branch until reaching Mott Avenue in Far Rockaway.

The Glendale Cut-off ran south from the Main Line at Rego Park to the Montauk Branch at Glendale. There it became the Rockaway Beach Branch, running south across Jamaica Bay to Hammels and west to Rockaway Park. The Rockaway Beach Branch south of Ozone Park is now the IND Rockaway Line of the New York City Subway.

The Creedmoor Branch was a short branch from the Main Line at Floral Park northwest to Creedmoor.

The Mineola-West Hempstead Branch ran north of the terminus of the West Hempstead Branch across NY 24 to Country Life Press Station where it briefly joined the Hempstead Branch then ran north of the Garden City Secondary towards a wye at Mineola Station with one branch that terminated at the station and another that crossed the main line and ended at the southern terminus of the Oyster Bay Branch.

The Bethpage Branch ran north from the Main Line and Central Branch at Bethpage.

The Camp Upton Branch was a short branch north from the Main Line to Camp Upton.

The Manorville Branch or Manor Branch ran from the Main Line at Manorville southeast to the Montauk Branch at Eastport.

The Northport Branch ran northeast of the current Port Jefferson Branch between Greenlawn and Northport Village.

The Wading River Branch ran east from Port Jefferson to Wading River, serving the towns of Mount Sinai, Miller Place, Rocky Point, and Shoreham.

The Sag Harbor Branch ran north from the Montauk Branch at Bridgehampton to Sag Harbor.