The order of the books is:
1. The Maze of Bones
2. The Sword Thief
3. The Cahills vs. Vespers
4. The Secret of the Old Clock
5. The Curse of the Cave
6. The Serpent's Shadow
7. The Black Pyramid
8. Beyond the Grave
9. The Vanishing of the Vespers
10. The Sword
11. The Cipher
12. The Emperor's Code
13. The Last Oracle
14. The Scorpio Races
15. The Crown of Ptolemy
16. The Iron Trial
Let me know if you have any other questions about The 39 Clues!