The plant-parasitic nematodes Pratylenchus penetrans and Heterodera glycines are of major economic importance worldwide. Here, we present a survey of over 1,900 expressed sequence tags (ESTs) for P. penetrans and of almost 22,000 ESTs for H. glycines. Furthermore, we conducted microarray expression profiling for over 6,800 H. glycines genes throughout the life cycle. We identified over 600 H. glycines genes that encode secretory proteins and provide microarray data for all known H. glycines parasitism genes as well as for H. glycines genes with similarity to known plant and microbe sequences. In order to extend these studies, we have identified soybean and Phytophthora sojae sequences that consistently cross-hybridize in microarray analyses with probes derived from H. glycines mRNA and identified H. glycines ESTs potentially responsible for this cross-hybridization. The impact of these findings on our understanding of host-parasite relationships is discussed. Furthermore, we showed that H. glycines parasitism proteins with nuclear localization signals are imported into plant cell nuclei. Using the same approach, we also confirmed the predicted nuclear localization for the cyst nematode-responsive soybean transcription factor GmEREBP1.