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Original list by JJ87
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Updated by Kiekan
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Last Updated: 9.14.2015
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VOLUME 1
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Marvel Masterworks vol. 11-10
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Marvel Masterworks vol. 211-19
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Marvel Masterworks vol. 320-30
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Marvel Masterworks vol. 431-40
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Marvel Masterworks vol. 541-50
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Marvel Masterworks vol. 651-61
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Marvel Masterworks vol. 762-67
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Marvel Masterworks vol. 868-77
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Marvel Masterworks vol. 978-87
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Marvel Masterworks vol. 1088-99
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Marvel Masterworks vol. 11100-109
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Marvel Masterworks vol. 12110-120
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Marvel Masterworks vol. 13121-131
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Marvel Masterworks vol. 14132-142
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Marvel Masterworks vol. 15143-155
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Marvel Masterworks vol. 16156-168
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Marvel Masterworks vol. 17169-180176-180 were also reprinted in: A New Goblin
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UNCOLLECTED181-192
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Return of the Burglar193-200
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UNCOLLECTED201-203
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Spider-Man vs Black Cat204-205
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Spider-Man Visionaries: Roger Stern206
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UNCOLLECTED207-223
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Nothing Can Stop the Juggernaut224-230
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Mark of the Tarantula231-237
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Origin of the Hobgoblin238-239
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UNCOLLECTED240-244
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Origin of the Hobgoblin244-245
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UNCOLLECTED246-248
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Origin of the Hobgoblin249-251
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The Complete Alien Costume Saga Book 1252-258
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The Complete Alien Costume Saga Book 2259-263
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Ghosts of the Past Epic Collection259-272
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Secret Wars II Omnibus273-274
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UNCOLLECTED275-278
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Spider-Man vs. Silver Sable279-281
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UNCOLLECTED282-289
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The Wedding290-292
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Kraven's Last Hunt293-294
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Life in the Mad Dog Ward295
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UNCOLLECTED296-297
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Spider-Man Visionaries: Todd McFarlane298-305
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Spider-Man Legends Vol 2: Todd McFarlane306-314
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Spider-Man Legends Vol 3: Todd McFarlane315-319(Also includes 320-323, 325 and 328)
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The Assassin Nation Plot320-325
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Cosmic Adventures Epic Collection326-333
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Sinister Six334-339
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UNCOLLECTED340-343
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Vengeance of Venom344-347
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Spider-Man: Am I an Avenger?348
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Spider-Man vs. Doctor Doom349-350
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Round Robin Epic Collection351-360
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Spider-Man: Carnage361-363
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UNCOLLECTED364
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Very Best of Spider-Man365
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UNCOLLECTED366-367
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Invasion of the Spider Slayers368-373
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Vengeance of Venom374-375
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UNCOLLECTED376-377
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Maximum Carnage378-380
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UNCOLLECTED381-393
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The Complete Clone Saga Epic Vol. 1394
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The Complete Clone Saga Epic Vol. 2395-399
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The Complete Clone Saga Epic Vol. 3400-401
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The Complete Clone Saga Epic Vol. 4402-404
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The Complete Clone Saga Epic Vol. 5405-406
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The Complete Ben Reilly Epic Vol. 1
Containes spider books that were retitled "Scarlet Spider", i.e. "Amazing Scarlet Spider"
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The Complete Ben Reilly Epic Vol. 2407-408
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The Complete Ben Reilly Epic Vol. 3409-410
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The Complete Ben Reilly Epic Vol. 4411-413
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The Complete Ben Reilly Epic Vol. 5414-416
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The Complete Ben Reilly Epic Vol. 6417-418
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UNCOLLECTED419
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X-Man: Dance with the Devil420
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UNCOLLECTED421-431
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Spider-Hunt432-433
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Identity Crisis434-435
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UNCOLLECTED436-439
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Gathering of Five440-441
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NOTES:
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-The Spider-Man by Roger Stern Omnibus collects #206 and #224-252.
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-The Amazing Spider-Man by Michelinie /McFarlane Omnibus collects #296-329.
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These omnis fill in some gaps that are listed as "Uncollected" above.
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VOLUME 2
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 (#1-58, which is the same as #442-499 in original numbering)
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The Next Chapter Vol. 11-6
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The Next Chapter Vol. 27-12
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The Next Chapter Vol. 313-19
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UNCOLLECTED20-24
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Revenge of the Green Goblin25
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UNCOLLECTED26-29
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JMS Ultimate Collection, Book 130-45
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JMS Ultimate Collection, Book 246-58