Purification of polygalacturonase (PG) from the cultures of Aspergillus carbonarius obtained by acetate buffer extraction after solid-state fermentation was attempted by integrated membrane process and alginate affinity precipitation. The carbohydrates were completely eliminated (98%-99%) with a PG recovery of 72%-80% during integrated membrane process, which would otherwise interfere with the purification process and lead to enzyme loss. However, specific activity of PG did not improve (1.19-1.21 fold) due to the presence of other similar molecular mass proteins. Under optimum conditions of affinity precipitation, the specific activity of PG enhanced to 2450 U/mg (4 fold) with almost complete elimination of carbohydrates and colour compounds resulting in a PG recovery of 61%. PG purity obtained with ultrafiltration (UF) was comparable with the conventional dialysis during desalting eluted PG, besides UF rendered a concentrated PG. The enzyme purity stated was as descend by SDS-PAGE. The results suggested suitability of affinity precipitation for PG purification from solid-state cultures and the potential of UF as a single step process for handling eluted PG. (C) 2009, The Society for Biotechnology, Japan. All rights reserved.