Base Set: 430 cards (one series; last 30 cards exclusive to factory sets)
- Glossy: 400 cards (1:12 Hobby, 1:24 retail)
- Glossy Gold: 400 cards (1:144)
- Awards Winners: 6 cards*
- Lumber Company: 25 cards*
- Smoke 'n Heat: 15 cards*
- Smooth Leather: 14 cards*
- Team Leaders: 30 cards*
- Top 40: 40 cards (two-per-pack, fat pack exclusive)
- Stars of Tomorrow: 10 cards (1:10)
- Team Fleer: 15 cards (1:360)
- Autographics: 9 cards (1:432)
- Fleer Fabrics: 42 cards (1:36 Hobby, 1:72 retail)
Notable Cards: The dozens of factory-set exclusive parenth-RCs.
- First Fleer Baseball set produced by Upper Deck.
- Five years after Fleer-Skybox screwed over set builder by issuing a factory set with additional base set cards, Upper Deck issues a factory set with additional base set cards. Although in UD's defense, 2006 was the first year the MLBPA limited the number of releases to 20, and a dedicated Update set would have counted against that figure.
- First year of the MLBPA's "ROOKIE CARD" icon program; however, most 2006 Fleer cards bearing that icon are not "true" RCs.
Full Set (factory): $50 (NmMT)
2006 Fleer Tradition
Base Set: 200 cards (one series)
- Sepia: (1:3 Hobby, 1:18 retail)
- Black & White: (1:9 Hobby, 1:36 retail)
- Press Plates: (1:288, Hobby exclusive)
- 1934 Goudey Greats: 100 cards (1:36, Hobby Exclusive)
- Blue Chip Prospects: 25 cards (1:6 Hobby, 1:18 retail)
- Diamond Tribute: 25 cards (1:9 Hobby, 1:36 retail)
- Grass Roots: 25 cards (1:6 Hobby, 1:36 retail)
- Triple Crown Contenders: 15 cards (1:9 Hobby, 1:36 retail)
- Ken Griffey, Jr. 1989 Fleer Autographed Buyback: 1 card (Hobby exclusive, numbered to 99)
- Traditional Threads: 41 cards (1:41 Hobby, 1:108 retail)
- Signature Tradition: 2 cards (1:1269, Hobby exclusive)
Notable Cards: Kenji Johjima and Jon Lester RCs, Ryan Zimmerman, Jonathan Papelbon parenth-RCs.
- In lieu of releasing an Update set, Upper Deck released this one-off product. They probably would have done better if they went with the Update set.
- Much like the 2002, Upper Deck released both a "Fleer Baseball" and "Fleer Tradition Baseball" sets. Unlike 2002, '06 Fleer Baseball is considered to be part of the Fleer/Fleer Tradition "lineage," while '06 Fleer Tradition should not.
- A design that borrows from various Topps sets from the 60s, 70s, and 80s.
- First Fleer set with Press Plates.