A techno-economic analysis of submerged (SmF) and solid state fermentation (SSF) processes for Aspergillus carbonarius polygalacturonase production was performed to make an appropriate process selection. The downstream processing involved integrated membrane process (IMP) and alginate affinity precipitation (AAP). For a production scale of 30 kL purified polygalacturonase concentrate per year, the total upstream cost of SmF was 14% lower than the SSF process. Downstream processing cost by IMP was 47% lower than AAP. The SmF-IMP process required a total capital investment that was 15-24% lower than the SmF-AAP and SSF-AAP processes. The corresponding unitary product cost was also lower by 24-36% in SmF-IMP process. Thus the SmF-IMP process proved to be very attractive from an economic point of view. (C) 2012, The Society for Biotechnology, Japan. All rights reserved.