The relationship between fungal morphology and heterologous protein production was examined for an Aspergillus awamori strain during a series of fermentations with a batch phase followed by a fed-batch phase. Agitation rate and inoculation concentration were used as controlled variables to generate different fungal morphologies in 20-dm3 stirred tank reactors. Morphology was quantitatively characterized using Image Analysis. The different agitation rates and inoculum concentrations had large effects on the development in hyphal length and number of tips during the fermentations. A reduced inoculum concentration resulted in a more branched mycelium. The different agitation rates affected the morphology after 30 h of fermentation significantly but did not affect the start time of fragmentation. A 3-fold increase in hyphal length increased the apparent viscosity by a factor of 7. The observed morphological differences had only a limited effect on product formation, suggesting that the structural features such as hyphal length and number of tips are of less importance for product formation. The primary effect of morphology on product formation is due to viscosity.