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ISO 3166:1974 was first published in 1974. It was descended from the distinguishing signs for vehicles under the Conventions on Road Traffic of 1949 and 1968. It has been modified as needed over the years, and updated with new editions in 1981, 1988, and 1993. One source says that the three-digit codes first appeared in the 1981 edition. In 1996, it was announced that the standard would be divided into three parts. ISO 3166-1 would continue to provide two-letter, three-letter, and three-digit codes for countries. ISO 3166-2 would contain codes for primary administrative subdivisions of countries. ISO 3166-3 would provide codes for obsolete country names (those deleted from ISO 3166 since 1974). The first publication of ISO 3166-1 was dated 1997.

The following timeline lists all the changes I could find that have affected the names or the codes for any entity. In most cases I haven't mentioned the code values following a change, because they can be looked up in the Country Codes table, or sometimes farther down the timeline.

1. 1975: Sikkim (codes SK, SKM) merged with India.
2. ~1976: Three-letter code for Philippines changed from PHI to PHL.
3. 1977: North Vietnam (codes VD, VDR, full name Democratic Republic of Viet-Nam) merged with South Vietnam (VN, VNM, full name Republic of Viet Nam) to form Vietnam.
4. 1977: Name of French Territory of the Afars and Issas (codes AI, AFI, 262) changed to Djibouti.
5. 1977: Name of Dahomey (codes DY, DHY, 204) changed to Benin.
6. 1979: French Southern and Antarctic Territories (codes FQ, ATF) split into French Southern Territories and a section corresponding to Adélie Land, which was not given an entry because it was considered part of Antarctica.
7. 1979: British Antarctic Territory (codes BQ, ATB) merged with Antarctica.
8. 1979: Gilbert and Ellice Islands (codes GE, GEL, 296) split into Kiribati and Tuvalu.
9. 1980: Southern Rhodesia (alpha codes RH, RHO, 716) changed to Zimbabwe.
10. 1980: Name of New Hebrides (codes NH, NHB, 548) changed to Vanuatu.
11. 1980: Panama Canal Zone (codes PZ, PCZ) merged with Panama.
12. 1983: Dronning Maud Land (codes NQ, ATN, 216) merged with Antarctica.
13. 1984: Canton and Enderbury Islands (codes CT, CTE, 128) merged with Kiribati.
14. 1984: Name of Upper Volta (codes HV, HVO, 854) changed to Burkina Faso.
15. ~1985: Saint Kitts-Nevis-Anguilla (codes KN, KNA, 658) split into Anguilla and "Saint Kitts and Nevis".
16. ~1985: Official English name of Spanish Sahara changed to Western Sahara.
17. ~1986: Aruba split from Netherlands Antilles.
18. 1986: Trust Territory of the Pacific Islands (codes PC, PCI, 582) split into Federated States of Micronesia, Marshall Islands, Northern Mariana Islands, and Palau.
19. 1986: United States Minor Outlying Islands formed by merging Johnston Atoll (codes JT, JTN, 396), Midway Islands (MI, MID, 488), United States Miscellaneous Pacific Islands (PU, PUS, 849), and Wake Island (WK, WAK, 872).
20. 1989-12-05 (Newsletter III-1): Official English name of Burma (codes BU, BUR, 104) changed to Myanmar.
21. 1990-08-14 (Newsletter III-7): People's Democratic Republic of Yemen (short name, Democratic Yemen; codes, YD, YMD, 720) merged with Yemen Arab Republic (short name, Yemen). Numeric code changed from 886 to 887. Short name changed to Republic of Yemen.
22. 1990-08-14 (Newsletter III-10): Official English name of Kampuchea changed to Cambodia.
23. 1990-10-30 (Newsletter III-13): German Democratic Republic (codes DD, DDR, 278) merged with Federal Republic of Germany. Numeric code changed from 280 to 276.
24. 1992-04-19 (Newsletter III-22): Official English name of Micronesia changed to Federated States of Micronesia.
25. 1992-04-19 (Newsletter III-23): Full name (Ukrainian Soviet Socialist Republic) and short name (Ukrainian S.S.R.) changed to Ukraine. No codes changed. (Note: although Belarus and Ukraine were as much a part of the Soviet Union as any of the other constituent republics, they had their own seats in the U.N. General Assembly, and consequently their own ISO codes, during the Soviet period.)
26. 1992-06-15 (Newsletters III-16, 17, 18, 27, 29, 30, 31, 32, 33, 34, 35, 36): Armenia, Azerbaijan, Estonia, Kazakstan, Kyrgyzstan, Latvia, Lithuania, Moldova, Russian Federation, Tajikistan, Turkmenistan, and Uzbekistan split from U.S.S.R.
27. 1992-06-15 (Newsletter III-19): Full name (Byelorussian Soviet Socialist Republic) and short name (Byelorussian S.S.R.) changed to Belarus; its three-letter code changed from BYS to BLR.
28. 1992-06-15 (Newsletter III-26): Croatia split from Yugoslavia.
29. 1992-08-28 (Newsletter III-28): Georgia split from U.S.S.R.
30. 1992-08-30 (Newsletter III-37): U.S.S.R. (full name Union of Soviet Socialist Republics, codes SU, SUN, 810) removed from list.
31. ~1993 (Newsletter III-39): Bosnia and Herzegovina split from Yugoslavia.
32. 1993-06-15 (Newsletter III-38): Slovenia split from Yugoslavia.
33. 1993-06-15 (Newsletters III-49 through III-51): Czechoslovakia (full name Czechoslovak Socialist Republic, codes CS, CSK, 200) split into Czech Republic and Slovakia.
34. 1993-06-18 (Newsletter III-24): Metropolitan France (codes FX, FXX, 249) added. The standard didn't specify the geographical compass of this entity, but it was clearly intended to represent France in European, including Corsica. The entity was later removed from the list (see 1997-07-14).
35. 1993-07-02 (Newsletter III-52): Full name of Angola changed from People's Republic of Angola to Republic of Angola.
36. 1993-07-12 (Newsletter III-40): Official English name of Republic of Yemen changed to Yemen.
37. 1993-07-12 (Newsletter III-46): Neutral Zone (between Saudi Arabia and Iraq, codes NT, NTZ, 536) removed from list. The Neutral Zone was split up and merged with Saudi Arabia and Iraq following the Gulf War of 1991.
38. 1993-07-12 (Newsletter III-47): Numeric code of Netherlands Antilles changed from 532 to 530 (a delayed consequence of the splitting off of Aruba).
39. 1993-07-12 (Newsletter III-48): Mayotte added to list. It apparently was previously considered part of France, but the standard never said so explicitly.
40. 1993-07-12 (Newsletter III-53): Full name of Madagascar changed from Democratic Republic of Madagascar to Republic of Madagascar.
41. 1993-07-16 (Newsletters III-55 and III-56): Eritrea split from Ethiopia; numeric code of Ethiopia changed from 230 to 231.
42. 1993-07-16 (Newsletter III-57): The Former Yugoslav Republic of Macedonia split from Yugoslavia.
43. 1993-07-16 (Newsletter III-58): Full name of Afghanistan changed from Democratic Republic of Afghanistan to Islamic State of Afghanistan.
44. 1993-07-22 (Newsletter III-44): Numeric code of Panama changed from 590 to 591 (a delayed consequence of the merging with the Panama Canal Zone).
45. 1993-07-23 (Newsletter III-54): South Georgia and the South Sandwich Islands split from Falkland Islands.
46. 1993-07-25 (Amendment to Newsletter III-32): Official English name of Kyrgyzstan changed to Kyrgyz Republic.
47. 1993-07-28 (Newsletter III-45): Numeric code of Yugoslavia changed from 890 to 891 (a consequence of the splitting off of Bosnia and Herzegovina, Croatia, Macedonia, and Slovenia).
48. 1994-01-26 (Newsletter III-59): Full name of Andorra changed from Andorra to Pricipality of Andorra.
49. 1994-01-26 (Newsletter III-60): Full name of Cambodia changed to Kingdom of Cambodia.
50. 1996-04-03 (Newsletter IV-1): Short and full names of Vatican City changed from Vatican City State (Holy See) to Holy See (Vatican City State).
51. 1997-07-14 (Newsletter IV-2): Zaire (full name Republic of Zaire, alpha codes ZR, ZAR) changed to The Democratic Republic of the Congo.
52. 1997-07-14: Metropolitan France removed from the list, but remains an "exceptionally reserved code element".
53. 1998-02-05 (Newsletter V-1): Formal name of Samoa changed from Independent State of Western Samoa to Independent State of Samoa.
54. 1999-10-01 (Newsletter V-2): Occupied Palestinian Territory split from Israel.
55. 2002-02-01 (Newsletter V-3): Three-letter code for Romania changed from ROM to ROU.
56. 2002-05-20 (Newsletters V-4 and V-5): Official English spellings of two country names were changed: Kazakstan to Kazakhstan, and Macau to Macao. The ISO two- and three-letter codes for East Timor were changed from TP to TL and from TMP to TLS, respectively.
57. 2002-11-15 (Newsletter V-6): Official English name of East Timor changed to Timor-Leste.
58. 2003-01-14 (Newsletter V-7): Formal name of Comoros changed from Islamic Federal Republic of the Comoros to Union of the Comoros.
59. 2003-07-23 (Newsletter V-8): Official English name of Yugoslavia changed to Serbia and Montenegro. The alpha codes were changed from YU, YUG to CS, SCG.
60. 2004-02-13 (Newsletter V-9): Åland Islands split from Finland. No code change for Finland.
61. 2006-03-29 (Newsletter V-11): Guernsey, Isle of Man, and Jersey split from United Kingdom. No code change for United Kingdom.
62. 2006-09-26 (Newsletter V-12): "Serbia and Montenegro", whose codes were (CS, SCG, 891), split into two countries: Serbia and Montenegro.
63. 2007-09-21 (Newsletter VI-1): Saint Barthélemy and "Saint-Martin (French part)" split from Guadeloupe. No code change for Guadeloupe.
64. 2008-03-31 (Newsletter VI-2): Short name of Republic of Moldova changed to Moldova.
65. 2008-09-09 (Newsletter VI-3): Formal name of Nepal changed to Federal Democratic Republic of Nepal.
66. 2009-01-07 (Newsletter VI-4): Reversed the change to Moldova in Newsletter VI-2.
67. 2009-03-03 (Newsletter VI-5): Short name of Venezuela changed to Bolivarian Republic of Venezuela.
68. 2009-05-08 (Newsletter VI-6): Name of Bolivia changed to Plurinational State of Bolivia (both short and formal).
69. 2010-02-22 (Newsletter VI-7): Short name of Saint Helena changed to Saint Helena, Ascension and Tristan da Cunha.
70. 2010-12-15 (Newsletter VI-8): Curaçao and "Sint Maarten (Dutch part)" split from Netherlands Antilles, which was renamed "Bonaire, Saint Eustatius and Saba". The codes for Netherlands Antilles (AN, ANT, 530) were retired.
71. 2011-06-12 (Newsletter VI-9): "Saint" changed to "Sint" in the English name of Bonaire; formal name of Fiji changed to "Republic of Fiji"; formal name of Myanmar changed to "Republic of the Union of Myanmar"; formal name of Niue changed to Niue, deleting "Republic of".
72. 2011-08-09 (Newsletter VI-10): South Sudan split from Sudan. Sudan's former N-3 code, 736, was retired. The other codes for Sudan remained unchanged.
73. 2011-11-08 (Newsletter VI-11): Short name of Libya changed to Libya, deleting "-n Arab Jamahiriya".
74. 2012-02-15 (Newsletter VI-12): Formal name of Hungary changed to Hungary, deleting "Republic of".
75. 2012-08-02 (Newsletter VI-13): Formal name of Eritrea changed to State of Eritrea.
76. 2013-02-06 (Newsletter VI-14): Name of Palestine changed from "Occupied Palestinian Territory" to "State of Palestine" (both short and formal).

Sources:

Change history from 1989 to 1994 comes from a document attributed to the RIPE Network Coordination Centre. (RIPE = Réseaux IP Européens = European IP Networks.) Many copies of this document, with different update dates, exist on the Web. Some examples are here , here , and here . I have not actually seen the original newsletters, so I can't explain the discrepancy between their serial numbers and dates; there may be errors in the RIPE document. Change history from 1996 on comes from documents I have seen, in either printed or electronic form. Change history prior to 1989 is reconstructed from various printed and online documents, and may have some small mistakes.