Fungal pellet formation is an important topic of fermentation research. It has been reported that many factors such as agitation, medium nutrients, pH, polymer additives, and inoculum size influence the formation of fungal pellets. However, a few studies on the effects of all of these factors on fungal pellet formation have been reported. This paper conducted a comprehensive investigation using a completely randomized design (CRD) on a filamentous fungus, Rhizopus oryzae NRRL 395, in order to discover the effects of the above factors on fungal pellet formation. In addition, other factors, such as addition of biodegradable polymers and spore storage time that have not been reportedly studied were examined and their effects on pellet formation were investigated. A multiple logistic regression model was established to predict the probability of pellet formation using the above factors and their interactions as predictor variables. Model building and diagnostics were obtained using the Statistical Analysis System (SAS 9.0) program. The model developed in this study can be used to predict the pellet formation of other R. oryzae strains as well.