BACKGROUND: The objective of the present work is to report an efficient pre-treatment process for sunflower oil biodiesel raw glycerol (SOB-RG) and its fermentation to 1,3-propanediol. RESULTS: The growth inhibition percentages of Clostridium butyricum DSM 5431 on grade A (pH 4.0) and grade B (pH 5.0) phosphoric acid-treated SOB-RG were similar to those of pure glycerol at 20 g glycerol L-1; i.e., 18.5 +/- 0.707% to 20.5 +/- 0.7% inhibition. In grade A, growth inhibition was reduced from 85.25 +/- 0.35% to 32 +/- 1.4% (a 53.25% reduction) at 40 g glycerol L-1 by washing grade A raw glycerol twice with n-hexanol (grade A-2). The kinetic parameters for product formation and substrate consumption in anaerobic batch cultures gave almost similar values at 20 g glycerol L-1, while at 50 g glycerol L-1 volumetric productivity (Q(p)) and specific rate of 1,3-propanediol formation (q(p)) were improved from 1.13 to 1.85 g L-1 h(-1) and 1.60 to 2.65 g g(-1) h(-1), respectively, by employing grade A-2 raw glycerol, while the yields were similar (0.5-0.52 g g(-1)). CONCLUSION: The results are important as the pre-treatment of SOB-RG is necessary to develop bioprocess technologies for conversion of SOB-RG to 1,3-propanediol. (C) 2008 Society of Chemical Industry.