Technical Abstract: The roots of susceptible 14 day-old soybean plants (cv. Williams) were inoculated with J2 soybean cyst nematodes, Heterodera glycines. After 8, 12 and 16 dpi the roots were placed under a stereomicroscope and root pieces (1 to 5 mm) that displayed 1 to many swollen SCN females were dissected out, lateral roots trimmed off, and colleted into liquid nitrogen. Similar root pieces were collected from roots that were not inoculated and kept for 8, 12, and 16 days. RNA was collected from replicate samples and hybridized to Affymetrix soybean GeneChips. Approximately 76% of 37,593 probe sets on the GeneChip indicated above background (p<0.05) expression in SCN inoculated and non-inoculated root pieces. When SCN inoculated is compared to non-inoculated roots, less than 3% and 0.5% of the hybridization signals to probe sets change more than 4-fold and 8-fold, respectively. Clustering of probe sets based on functional grouping indicate notable increases in probe sets associated with histones, disease and defense, and cell wall enzymes. A notable decrease was observed for proteins associated with ion and substrate transporters.