The subject of this monograph is the quaternionic spectral theory based on the notion of S-spectrum. With the purpose of giving a systematic and self-contained treatment of this theory that has been developed in the last decade, the book features topics like the S-functional calculus, the F-functional calculus, the quaternionic spectral theorem, spectral integration and spectral operators in the quaternionic setting. These topics are based on the notion of S-spectrum of a quaternionic linear operator. Further developments of this theory lead to applications in fractional diffusion and evolution problems that will be covered in a separate monograph.