Phytoplasmas belong to the Class Mollicutes and are non-culturable intra- and extracellular bacterial pathogens of insects and plants. Various computer algorithms were employed to mine the near complete genome sequence of phytoplasma strain AY-WB for genes encoding potential virulence factors. So far, 56 candidate virulence proteins were selected for functional analysis. To determine whether these proteins affect plants, corresponding genes were cloned into the binary potato virus X expression vector, pGR106, and expressed in tomato and Nicotiana benthamiana via Agrobacterium-mediated inoculation. This revealed 16 phytoplasma proteins that induced morphological aberrations in plants. Interestingly, five of the 16 proteins contain nuclear localization signals. Localization studies using yellow fluorescence protein fusions showed that two of the five proteins target plant cell nuclei. Transcripts of genes of these two proteins were detected in plants during AY-WB infection. To allow immunolocalization of these AY-WB proteins in the leafhopper vector and plant hosts, genes were expressed in Escherichia coli for subsequent antibody synthesis.