PEP-II consists of two independent storage rings in the tunnel that housed the original PEP collider. The high-energy ring, which stores a 9 GeV electron beam, is an upgrade of the existing PEP collider, while the low-energy ring, in which the 3.1 GeV positrons are stored, is completely new.

Matter and anti-matter are thought to have been created in equal amounts in the Big Bang, and should have completely annihilated each other. However, we clearly live in a matter-dominated universe, which indicates that a small imbalance must have existed between matter and anti-matter at a very early stage in the universe. PEP-II will make measurements which, physicists hope, will clarify some of the competing theoretical models for this mechanism.