The effect of on-farm storage on microbial growth on baled and pelletised Brassica napus (oilseed rape/canola) straw was investigated. Canola straw collected in 2008 and 2009 was stored baled in an open shed for 3, 4, 7, 10 and 20 months in 2008 and for 1 and 3 months in 2009. Pellets were produced from straw stored for 3, 7, and 10 months in 2008 and straw stored for 3 months in 2009, and stored for up to 48 weeks. The moisture content (MC), water activity (a(w)), bacterial and fungal colony-forming units (CFU), and carbon-to-nitrogen ratio (C:N) of canola straw bales and pellets were measured during storage. In addition, temporal environmental conditions (ambient temperature and relative humidity) and bale temperature were monitored. The moisture content showed a tendency to stabilise during storage, with an equilibrium moisture content of approximately 155 g kg (-1) total weight for straw bales and 110 g kg (1) total weight for straw pellets. Consequently, the water activity of canola straw bales remained below 0.8 and that of pellets below 0.66 during storage, providing an explanation for relatively low microbial growth. The number of bacterial and fungal CFU present in the straw bales and pellets followed the trend of ambient relative humidity and no correlation was found with the C:N ratio of the biomass. Canola straw pellets were considered a superior combustion fuel to straw bales due to lower moisture content and less microbial deterioration during storage. (C) 2011 Elsevier Ltd. All rights reserved.