Published Collections
- Volume 1: Agatha Heterodyne and the Beetleburg Clank (96 pp) (reprints #1–3)
- Paperback: ISBN 1-890856-19-3, full color Paperback: ISBN 1-890856-50-9
- Hardcover: ISBN 1-890856-20-7
- Volume 2: Agatha Heterodyne and the Airship City (112 pp) (reprints #4–6)
- Paperback: ISBN 1-890856-30-4
- Hardcover: ISBN 1-890856-31-2
- Volume 3: Agatha Heterodyne and the Monster Engine (128 pp) (reprints #7–9)
- Paperback: ISBN 1-890856-32-0
- Hardcover: ISBN 1-890856-33-9
- Volume 4: Agatha Heterodyne and the Circus Of Dreams (128 pp) (reprints #10–13 + April–June 2005 webcomic)
- Paperback: ISBN 1-890856-36-3
- Hardcover: ISBN 1-890856-37-1
- Volume 5: Agatha Heterodyne and the Clockwork Princess (112 pp) (reprints webcomic)
- Paperback: ISBN 1-890856-39-8
- Hardcover: ISBN 1-890856-38-X
- Volume 6: Agatha Heterodyne and the Golden Trilobite (150 pp) (reprints webcomic)
- Paperback: ISBN 1-890856-42-8
- Hardcover: ISBN 1-890856-41-X
- Volume 7: Agatha Heterodyne and the Voice of the Castle (128 pp) (reprints webcomic)
- Paperback: ISBN 978-1-890856-45-8
- Hardcover: ISBN 978-1-890856-46-5
- Volume 8: Agatha Heterodyne and the Chapel of Bones (144 pp) (reprints webcomic) Winner of the 2009 Hugo Award for Best Graphic Story
- Paperback: ISBN 978-1-890856-47-2
- Hardcover: ISBN 978-1-890856-48-9
- Volume 9: Agatha Heterodyne and the Heirs of the Storm (144 pg) (reprints webcomic) Winner of the 2010 Hugo Award for Best Graphic Story
- Paperback: ISBN 978-1-890856-52-6
- Hardcover: ISBN 978-1-890856-51-9
- Volume 10: Agatha Heterodyne and the Guardian Muse (152 pg) (reprints webcomic) Winner of the 2011 Hugo Award for Best Graphic Story
- Paperback: ISBN 978-1-890856-53-3
- Hardcover: ISBN 978-1-890856-54-0
- Volume 11: Agatha Heterodyne and the Hammerless Bell (168 pg) (reprints webcomic)
- Paperback: ISBN 978-1-890856-55-7
- Hardcover: ISBN 978-1-890856-56-4
- Girl Genius Omnibus Edition Vol 1 (2006) (reprints v.1–3 in smaller, black & white edition)
- Paperback: ISBN 978-1-890856-40-3
- Girl Genius Omnibus Vol 1: Agatha Awakens (2012) (reprints v.1–3 in color edition)
- Hardcover: ISBN 978-0-7653-3132-8
Volume 5 as well as all future collections reprint the website content from where the comic series was discontinued.
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