Viz Media originally published the manga in comic book format before going directly to graphic novels. The former were broken up into parts composed of chapters. The comics were published in two versions:
- Regular: Flipped to read from left to right, with Evangelion in a stylized English font on the front cover.
- Special Collector's Edition: Preserved the original orientation and read from right to left. Evangelion was written in Japanese on the front cover, beneath which was the designation Special Collector's Edition.
Part 1 - regular
- Part 1 #1 (1997)
- Part 1 #6 (1998)
Part 1 - special collector's edition
- Part 1 #1 SCE (1997)
- Part 1 #2 SCE (1997)
- Part 1 #3 SCE (1997)
- Part 1 #4 SCE (1997)
- Part 1 #5 SCE (1998)
- Part 1 #6 SCE (1998)
Part 2 - special collector's edition
- Part 2 #2 SCE (1998)
- Part 2 #4 SCE (1998)
- Part 2 #5 SCE (1998)
Part 3 - regular
- Part 3 #5 (1998)
Part 3 - special collector's edition
- Part 3 #1 SCE (1998)
- Part 3 #2 SCE (1998)
- Part 3 #3 SCE (1998)
- Part 3 #4 SCE (1998)
Part 5 - regular
- Part 5 #1 (2000)
- Part 5 #2 (2000)
- Part 5 #3 (2000)
- Part 5 #4 (2001)
- Part 5 #5 (2001)
- Part 5 #6 (2001)
- Part 5 #7 (2001)
Part 6 - REGULAR
- Part 6 #1 (2001)
- Part 6 #2 (2001)
Part 6 - SPECIAL COLLECTOR'S EDITION
- Part 6 #1 SCE (2001)
- Part 6 #2 SCE (2001)
- Part 6 #3 SCE (2001)
- Part 6 #4 SCE (2001)
Part 7 - REGULAR
- Part 7 #1 (2002)
- Part 7 #2 (2002)
- Part 7 #5 (2002)
Part 7 - SPECIAL COLLECTOR'S EDITION
- Part 7 #3 SCE (2002)
- Part 7 #4 SCE (2002)