In this study, we evaluated the use of an up-flow anaerobic sludge blanket (UASB) reactor to treat crude glycerol obtained from cottonseed biodiesel production. The laboratory-scale UASB reactor (7.0 L) was operated at ambient temperature of 26.5°C with chemical oxygen demand (COD) concentrations between 0.5 and 8.0 g/L. The volatile fatty acid contents, pH, inorganic salt contents and biogas production were monitored during a 280-day experimental period. Molecular biology techniques were used to assess the microbial diversity in the bioreactor. The reactor achieved COD removal efficiencies of up to 92% except during one phase when the efficiency decreased to 81%. Biogas production remained stable throughout the experimental period, when the fraction converted to methane reached values as high as 68%. The profile of the denaturing gradient gel electrophoresis (DGGE) bands suggested slight changes in the microbial community during reactor operation. The overall results indicated that the crude glycerol from biodiesel production can serve as a suitable substrate for anaerobic degradation with a stable reactor performance and biogas production as long as the applied organic loads are up to 8.06 kg COD/m3·d.