Giant cells induced by root-knot nematodes are highly specialized cells which function as transfer cells and provide nutrients to support the growth and reproduction of the nematode. Changes in the overall pattern of gene expression in giant cells occur during the formation and maintenance of the nematode feeding cells. Differential display analysis has been carried out to detect changes in gene expression in giant cells induced in tomato roots by Meloidogyne javanica, using mRNA isolated directly from mature giant cell cytoplasm, compared to non-infected root tissue. Eighty-one differential displayed bands were generated, and of these, 73 were up-regulated and 8 were down-regulated. Twenty-seven sequences were obtained by direct sequencing of the bands, and 16 fragments were further analysed by real-time quantitative RT-PCR. The most highly up-regulated transcript increased 56-fold in giant cells, and the greatest down-regulation was 11-fold. A time course of expression of the highest and lowest expressed transcripts was also undertaken by quantitative RT-PCR using giant cell enriched tissue. These showed similar changes in expression, but values were dramatically reduced. This result shows the importance of analysing giant cell cytoplasm directly, rather than starting with giant cell enriched tissue, to obtain accurate information on changes in gene expression in nematode feeding cells. Sequenced transcripts showed significant homology to mitogen-activated protein kinase, S-adenosylmethionine decarboxylase, cysteine synthase, cytochrome c reductase subunit, and ribosomal proteins. The expression analysed reflects the high metabolic rate in mature giant cells rather than processes of giant cell induction.