Morphology and citric acid production of an industrial strain of Aspergillus niger (R3) were investigated in 5 l fermentations using different inoculum types and agitation conditions. The fermentations were inoculated using dispersed and pelleted forms, and the effect on subsequent morphology and citric acid production in the 5 l fermenter were studied. The morphology was characterised in depth by automatic image analysis. Using on-line gas analysis by a mass spectrometer, and glucose, citric acid and oxalic acid analysis by an HPLC, some important metabolic parameters have been determined and compared for three citric acid fermentations. A relatively high yield of citric acid (0.74 g/g glucose) was obtained from a fermentation inoculated with dispersed mycelia. Two pelleted fermentations arose from pelleted inocula; one was conducted with low agitation in the early stages and the other with high agitation. With low agitation (300 rpm) the pellets of initial mean equivalent diameter 1.4 mm grew larger with fermentation time, until the agitation was increased at 96 h, to a very high level of 800 rpm when the pellets fragmented rapidly from 3.2 to 1.6 mm diameter. Both the citric acid yield (0.49 g/g glucose) and cell growth from this fermentation were very low. The glucose uptake rate, oxygen uptake rate (OUR), and carbon dioxide production rate (CPR) were also low compared to the non-pelleted fermentation although all showed a sharp rise after the fragmentation of the pellets. The high agitation speed of the second pelleted fermentation (500–800 rpm) retarded continued pellet size increases. The mean equivalent diameter at inoculation was 1.4 mm and this rose to only 1.5 mm towards the end of the fermentation (168 h). Both the citric acid yield (0.58 g/g glucose) and cell growth were higher than those obtained from the fermentation with large pellets but were still lower than in the dispersed morphology case. These results support previous qualitative ideas that initial inoculum morphology and fermentation conditions have significant effects on the subsequent culture morphology and productivity of the citric acid fermentation. In the present work however, these effects have been quantified, particularly using image analysis to characterise morphology and using HPLC to measure concentrations of important broth components. This information will be valuable for optimisation and better control of the citric acid fermentation.