Letter prefixes for naval military vessels go back hundreds of years, specifically to the British Royal Navy's HMS (His or Her Majesty's Ship). Most of the other former British colonies adopted this form of naval prefix, adding in letters to distinguish their specific country. Canada has HMCS, New Zealand has HMNZS, and Australia has HMAS. The United States of America is the only one of the few former British colonies with an active navy that does not incorporate the 'His or Her Majesty'. (note, Saudi Arabia also uses HMS as a naval prefix)

The USS prefix for U.S. naval vessels has existed since the 18th century, at least by 1790. USS was not the standard way to prefix the name of a military vessel, however. In fact, there was no standard of prefix. Ships were commonly identified in documents and by a number of means.
  1. Ship type (U.S.** Frigate Enterprise*)
  2. Ship type, no country designation (Frigate Enterprise)
  3. Type of rigging (U.S. Barque Enterprise)
  4. Ship Function (Flag Ship Enterprise)
  5. United States Ship (USS Enterprise)
  6. 'ship' (Ship Enterprise)
  7. Name only (Enterprise)
** U.S. and United States were (and are) frequently interchangeable.

It was not until 1907 that President Theodore Roosevelt got tired of the lack of standardization in ship prefixes, and created an executive order to have the United States Navy standardize on 'USS'.

"In order that there shall be uniformity in the matter of designating naval vessels, it is hereby directed that the official designation of vessels of war, and other vessels of the United States Navy, shall be the name of such vessel, preceded by the words, United States Ship, or the letters U.S.S., and by no other words or letters."
--Executive Order 549, 8 January 1907.

The policy of a standard prefix of USS does not hold for every single vessel operating for the United States Navy; there are some exceptions, as reflected in the current Navy regulations:

  1. "The Chief of Naval Operations shall be responsible for ... the assignment of classification for administrative purposes to water-borne craft and the designation of status for each ship and service craft. ....
  2. Commissioned vessels and craft shall be called "United States Ship" or "U.S.S."
  3. Civilian manned ships, of the Military Sealift Command or other commands, designated "active status, in service" shall be called "United States Naval Ship" or "U.S.N.S."
  4. Ships and service craft designated "active status, in service," except those described by paragraph 3 of this article, shall be referred to by name, when assigned, classification, and hull number (e.g., "HIGH POINT PCH-1" or "YOGN-8")."
-- United States Navy Regulations, 1990, Article 0406.

Ships covered by Roosevelt's order include all those involved in World War I, World War II, and on. There still exists some differences in ship prefixes in official and non-official documents a century after Roosevelt's order; sometimes the ship is referred to as the official 'USS'; and sometimes the ship is referred to as the ship name alone (with or without a preceding 'The'). For example, Enterprise, the Enterprise, USS Enterprise

*Note: Enterprise is used only as an example, and reflects only the writer's affinity for Star Trek, not any actual history.

USS is also the prefix for ships in the United Federation of Planets' Starfleet, in the Star Trek universe. Stands for United Space Ship, United Star Ship, or United Space Star Ship, depending on which Original Series episode you prefer.