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From The TV IV

Secondary affiliation was a practice of network affiliated television stations in which they would carry some of the programs of another network. It was used mostly with new networks that did not have the clearances of the already established networks. Indirectly, the term has also applied to independent stations, usually UHF, that in the past carried network programming passed up by that market's regular ABC, CBS and NBC stations.

ABC and DuMont did not have full clearance across the United States in the 1950s, so in many markets, they were the secondaries on stations already affiliated with NBC and CBS. As ABC grew in popularity primary affiliated stations began to pop up in several larger markets, while DuMont was relegated to secondary status (some extra large markets, such as New York and Los Angeles had primary DuMont stations). DuMont never managed to get enough primary affiliates and eventually folded.

The practice was used to a lesser extent with FOX in the late 1980s and early 1990s and The WB and UPN in the late 1990s but with multichannel delivery systems such as cable and satellite out of market stations could be delivered to areas without a local affiliate so there wasn't as much of a need.

With the advent of digital television secondary affiliation has been made obsolete by digital sub-channels. The new smaller networks the CW and MyNetworkTV are often carried on sub-channels of medium-to-smaller market stations. WXTX/channel 54 in Columbus GA currently carries FOX as its primary and MyNetworkTV as a secondary.

Some of the more notable secondary affiliations of the past, along with their primaries:

Station	Channel	Market	Primary	Secondaries			Ended	Notes
WSB	8	Atlanta, GA	NBC	ABC			1951	Moved to ch. 2 in 1951, switched to ABC in 1980
KFMB	8	San Diego, CA	CBS	ABC			1956
WJHG	7	Panama City, FL	NBC	ABC	CBS	DuMont	1973	Had ABC as primary 1973-77
WEWS	5	Cleveland, OH	CBS	ABC	DuMont		1955	Switched to ABC after dropping DuMont
KPHO	5	Phoenix, AZ	CBS	NBC	ABC	DuMont	1955	went independent afterwards, became CBS again in 1995
WMAZ	13	Macon, GA	CBS	ABC			1982
WJLA	7	Washington, DC	ABC	CBS			1949
WJZ	13	Baltimore, MD	ABC	Dumont			1955	switched to CBS in 1995
WHDH	7	Boston, MA	CBS	ABC	Dumont		1957	switched to ABC in 1961; switched to CBS in 1972; switched to NBC in 1995
WDSU	6	New Orleans, LA	NBC	CBS	ABC	DuMont	1957