Radopholus similis is an important nematode pest on fruit crops in the tropics. Unraveling the transcriptome of this migratory plant-parasitic nematode can provide insight in the parasitism process and lead to more efficient control measures. For the first high throughput molecular characterization of this devastating nematode, 5,853 expressed sequence tags from a mixed stage population were generated. Adding 1,154 tags from the EST division of GenBank for subsequent analysis, resulted in a total of 7,007 ESTs, which represent approximately 3,200 genes. The mean G + C content of the nucleotides at the third codon position (GC3%) was calculated to be as high as 64.8%, the highest for nematodes reported to date. BLAST-searches resulted in about 70% of the clustered ESTs having homology to (DNA and protein) sequences from the GenBank database, whereas one-third of them did not match to any known sequence. Roughly 40% of these latter sequences are predicted to be coding, representing putative novel protein coding genes. Functional annotation of the sequences by GO annotation revealed the abundance of genes involved in reproduction and development, which reflects the nematode population biology. Genes with a role in the parasitism process are identified, as well as genes essential for nematode survival, providing information useful for parasite control. No evidence was found for the presence of trans-spliced leader sequences commonly occurring in nematodes, despite the use of various approaches. In conclusion, we found three different sources for the EST sequences: the majority has a nuclear origin, approximately 1% of the EST sequences are derived from the mitochondrial transcriptome, and interestingly, 1% of the tags are with high probability derived from Wolbachia, providing the first molecular indication for the presence of this endosymbiont in a plant-parasitic nematode.