BACKGROUND: The impact of inoculation on performance and subsequent community structure is a critical question in gas biofiltration processes. Thus, the aim of this study is to evaluate the impact of inoculation on biofilters packed with an inorganic medium and fed with a gaseous mixture (oxygenated and sulphur compounds). RESULTS: Inoculated biofilters (BF1 and BF2 duplicates) exhibit higher overall removal performances and lower removal height (oxygenated: 100% at 50 cm and sulphur: 55% at 100 cm) than control biofilters (PC) (oxygenated: 94% and sulphur: 39% at 100 cm). The concentration of compounds was measured along the bed height using two sampling lines. For each biofilter, the evolution of removal efficiency as a function of height differs and depends on the line considered. At steady-state, a divergence is observed between the bacterial communities of BFs that exhibited a similar stratification pattern of removal efficiency. CONCLUSION: Inoculation of biofilters seems to bring enough diversity to allow the emergence of fitted species resulting in higher pollutants removal and to strengthen the heterogeneity of biodegradation activities distribution along the column height. The divergence of the microbial community structure in BF samples can be explained by low selective pressure and high resource availability which influence the community composition. Copyright (c) 2012 Society of Chemical Industry