  We study decoherence in superconducting qubits due to quasiparticle tunneling
which is enhanced by two known deviations from the equilibrium BCS theory. The
first process corresponds to tunneling of an already existing quasiparticle
across the junction. The quasiparticle density is increased, e.g., because of
an effective quasiparticle doping of the system. The second process is
quasiparticle tunneling by breaking of a Cooper pair. This can happen at
typical energies of superconducting qubits if there is an extended
quasiparticle density inside the gap. We calculate the induced energy decay and
pure dephasing rates in typical qubit designs. Assuming the lowest reported
value of the non-equilibrium quasiparticle density in Aluminum, we find for the
persistent-current flux qubit decay times of the order of recent measurements.
Using the typical sub-gap density of states in Niobium we also reproduce
observed decay times in the corresponding Niobium flux qubits.
