The use of transgenic plants for the production of heterologous proteins for pharmaceutical applications has increased continuously, since this provides a viable alternative to traditional expression systems. The choice of the host crop for such recombinant proteins has a significant influence on downstream processing and overall process economics. Varieties with less oil and phenolic compounds generate a less complex extract, thus facilitating recovery and purification processes for the heterologous protein. Maize is a crop which has proved its potentia for the production of high levels of recombinant proteins. In this study, the aqueous extracts of the endosperm of six non-transgenic maize varieties were analyzed for evaluation of their potential as hosts for the production of recombinant proteins. This evaluation was based on the following parameters associated with downstream processing: extract filtrability, concentration of proteins, carbohydrates and phenolics compounds and flour oil content. The study of the extraction process was carried out using factorial design and response surface methodology. The argument for the selection of a specific maize variety is presented as well as a discussion of the optimum range of conditions for the minimization of compounds, which could negatively interfere with downstream processing operations. (c) 2005 Elsevier Ltd. All rights reserved.401033273336