Aspergillus sojae, which is used in the making of koji, a characteristic Japanese food, is a potential candidate for the production of polygalacturonase (PG) enzyme, which of a major industrial significance. In this study, fermentation data of an A. sojae system were modeled by multiple linear regression (MLR) and artificial neural network (ANN) approaches to estimate PG activity and biomass. Nutrient concentrations, agitation speed, inoculum ratio and final pH of the fermentation medium were used as the inputs of the system. In addition to nutrient conditions, the final pH of the fermentation medium was also shown to be an effective parameter in the estimation of biomass concentration. The ANN parameters, such as number of hidden neurons, epochs and learning rate, were determined using a statistical approach. In the determination of network architecture, a cross-validation technique was used to test the ANN models. Goodness-offit of the regression and ANN models was measured by the R 2 of cross-validated data and squared error of prediction. The PG activity and biomass were modeled with a 5-2-1 and 5-9-1 network topology, respectively. The models predicted enzyme activity with an R 2 of 0.84 and biomass with an R 2 value of 0.83, whereas the regression models predicted enzyme activity with an R 2 of 0.84 and biomass with an R 2 of 0.69.