We study the parity effect and transport due to quasiparticles in circuits comprised of many superconducting islands. We develop a general approach and show that it is equivalent to previous methods for describing the parity effect in their more limited regimes of validity. As an example we study transport through linear arrays of Josephson junctions in the limit of negligible Josephson energy and observe the emergence of the parity effect with decreasing number of non-equilibrium quasiparticles. Due to the exponential increase in the number of relevant charge states with increasing length, in multi-junction arrays the parity effect manifests in qualitatively different ways to the two junction case. The role of charge disorder is also studied as this hides much of the parity physics which would otherwise be observed. Nonetheless, we see that the current through a multi-junction array at low bias is limited by the formation of meta-stable even-parity states.PACS numbers: 73.23. Hk,85.25.Cp, In superconducting circuits of small dimensions, charging effects play an important role. On the one hand the Coulomb blockade leads to charge pinning and an effective suppression of electronic transport at low bias voltage. On the other hand the superconducting nature manifests in the parity effect, i.e. given a odd number of electrons on the superconductor there is one remaining quasiparticle dominating the transport properties in the low bias regime 1-8 . Strictly speaking this picture is true for equilibrium and very low temperatures. However if a non-equilibrium situation is imposed, e.g. by applying a finite bias voltage, the average number of quasiparticles may be increased. Recently such non-equilibrium quasiparticle effects have been investigated in superconducting qubits 9-14 and single electron transistors (SETs) [15][16][17][18][19] . In this context the interplay of charge transport, the excitation of non-equilibrium quasiparticles and the observation of the parity effect has been the subject of recent experiments with SETs 18 . Based on related theoretical modelling 19-21 we extend the prevailing transport theory of multi-junction circuits and show that this approach removes the ambiguities of previous approaches when including parity effects for more than one superconducting island, although our approach is equivalent to earlier work in the appropriate limits. As an example, we perform the first analysis of the parity effect in linear multijunction arrays and make a number of predictions for the electronic transport signatures that can be identified with the parity effect in these systems.