A morphologically structured model for the batch process of biomass growth and citric acid accumulation by Aspergillus niger is presented in this paper. The model consists of ten ordinary differential equations, which balance biomass and four physiological zones of hyphae, and includes the most important medium components, such as carbon sources, nitrogen source and citric acid. Digital analysis of microscopic images was employed to determine the hyphal fractions within each physiological zone. All model parameters were determined on the basis of data obtained in four experiments carried out in two types of bioreactors and under various process conditions, specifically normal and increased pressure. Some parameters were directly calculated from the experimental data by means of linear and non-linear regression. This allowed minimisation of the number of parameters to be found by means of an optimisation procedure, down to I I and thus, significantly reduced computation time. The simulated curves are largely consistent with the experimental data and some parameters appeared to be practically independent of process conditions. These findings contribute to the universality of the model proposed.