Distributed-phase-reference quantum key distribution stands out for its easy implementation with present day technology. For many years, a full security proof of these schemes in a realistic setting has been elusive. We solve this long-standing problem and present a generic method to prove the security of such protocols against general attacks. To illustrate our result, we provide lower bounds on the key generation rate of a variant of the coherent-one-way quantum key distribution protocol. In contrast to standard predictions, it appears to scale quadratically with the system transmittance.