Silicon heterojunction solar cells have demonstrated high efficiencies through excellent surface passivation. However, the use of amorphous silicon (a-Si) in the structure raises the question of long term stability as a-Si solar cells suffer degradation due to the Staebler-Wronski effect. The stability of a-Si in terms of its ability to passivate silicon wafers is evaluated by measuring the minority carrier lifetime and it is found to be unstable over time. The instability is most evident in thin, ∼ 10 nm, intrinsic a-Si only layers where lifetime falls from over 1ms immediately after annealing, to 300 μs one month later. The change in lifetime occurs even in the dark at room temperature with the largest fall in the first few days after deposition. The lifetime can be recovered close to its initial level by annealing the sample in air, indicating that the lifetime change is not due to a simple oxidation of the outer layer of a-Si. However, device measurements where an intrinsic/doped a-Si structure is used for the emitter and contact show no change in open circuit voltage or fill factor after one year. The changes in the passivation during processing has important implications for the sequence of device fabrication, the use of lifetime testing as a diagnostic tool and the passivation of all back contact devices.