Dan Boneh's "Introduction to Cryptography".
(Part 1) https://www.coursera.org/course/crypto (Part 2) https://www.coursera.org/course/crypto2
(Part 1) https://www.coursera.org/course/crypto (Part 2) https://www.coursera.org/course/crypto2
I also liked Udacity crypto course, less formal but with great "hands on" exercises: