The temperate pasture grass Lolium perenne L. is commonly found in association with the fungal endophyte Neotyphodium lolii. Viability of both seed and endophyte was evaluated by inoculation of individual genotypes from the host cultivar Bronsyn with six distinct endophyte strains. The resulting populations were subjected to either long-term storage under various temperature conditions, or accelerated ageing (AA) treatments. High temperature storage was detrimental to endophyte viability. The AA variables (relative humidity [RH] and time) and subsequent temperature and duration of storage significantly (P < 0.05) affected both seed germination and endophyte viability. Significant interaction effects between the AA treatment and storage conditions were also observed. Endophyte viability following AA treatment was inversely correlated with both increasing RH and duration of treatment. Differential responses between different endophytes within the Bronsyn host were also apparent. The standard endophyte (SE) strain and the novel endophytes AR1 and AR37 exhibited higher viability than NEA2, NEA3, and NEA6 during seed storage, suggesting the importance of identification and selection for compatible symbiotic associations in agronomic varieties. The observed similarity between assessments of endophyte viability after AA treatments and following long-term storage confirmed the capacity of moderate conditions (e.g. 80% RH for 7 days or 100% RH for 4 days) to predict variation in viability between different endophyte strains.