For all four viral and one parasite antigens tested in this study, partial products were common. The production of partial fragments in E. coli based IVTT reactions has been described previously and attributed to a phenomena called translational pausing but the presence of partial products did not adversely affect immunogenicity or antigenicity [46] . Since the antigens produced by E. coli based IVTT were at least partially insoluble, simple techniques for purification, such as antibody coated beads, were not effective. We therefore explored alternative purification options including Ni-NTA affinity resin and MagneHis Niparticles. Both purification systems tested using denaturating conditions proved efficient but a much higher product recovery was obtained with the Ni-NTA resin as compared to the MagneHis Ni-particles. Unexpectedly, with the eukaryotic based insect cell-free system, the solubility of the recombinants increased to almost 100%, but only two of the four proteins expressed in the E. coli cell-free system could be expressed in the insect cell based system, at least for the limited number of times expression was attempted. These data suggest that further studies with the insect cell-free system are warranted. Newer technologies of high throughput purification such as affinity ZipTips (Millipore, Ireland) and Ni-NTA plates (Qiagen, Valencia, CA) can facilitate the purification process, but do not effectively deal with solubility issues.