Fungal biofilters have been recently studied as an alternative to the bacterial systems for the elimination of hydrophobic volatile organic compounds (VOC). Fungi foster reduced transport limitation of hydrophobic VOCs due to their hydrophobic surface and extended gas exchange area associated to the hyphal growth. Nevertheless, one of their principal drawbacks is their slow growth, which is critical in the start-up of fungal biofilters. This work compares the use of different carbon sources (glycerol, 1-hexanol, wheat bran, and n-hexane) to reduce the start-up period and sustain high n-hexane elimination capacities (EC) in biofilters inoculated with Fusarium solani. Four parallel experiments were performed with the different media and the EC, the n-hexane partition coefficient, the biomass production and the specific consumption rate were evaluated. Biofilters were operated with a residence time of 1.3 min and an inlet n-hexane load of 325 g m−3reactor h−1. The time to attain maximum EC once gaseous n-hexane was fed was reduced in the three experiments with alternate substrates, as compared to the 36 days needed with the control where only n-hexane was added. The shortest adaptation period was 7 days when wheat bran was initially used obtaining a maximum EC of 160 g m−3reactor h−1 and a critical load of 55 g m−3reactor h−1. The results were also consistent with the pressure drop, the amount of biomass produced and its affinity for the gaseous n-hexane, as represented by its partition coefficient. Biotechnol. Bioeng. 2011; 108:758–765. © 2010 Wiley Periodicals, Inc.