The marked cellular changes during feeding site formation of the soybean cyst nematode (Heterodera glycines) indicate major changes in soybean gene expression. We used differential display of mRNA to detect host gene expression changes during the early compatible interaction between soybean and H. glycines. Fifteen cDNA clones corresponding to mRNAs with different abundances in H. glycines-infected versus uninfected roots were identified. Differential display results indicated that abundances of five mRNAs increased in infected roots, whereas abundances of 10 mRNAs decreased. Transcripts for nine of these 15 cDNAs could be detected on RNA blots, and their hybridization signals confirmed the differential display results for eight of these nine cDNAs. Sequence analyses identified five cDNAs with decreased mRNA levels in infected roots as corresponding to two putative aldolase genes, a transcription-factor TFIIA homologue, the soybean small GTP-binding protein gene sra1, and the soybean auxin down-regulated gene ADR12. RNA blot analyses of other auxin down-regulated genes revealed a decrease in their mRNA abundances in H. glycines-infected roots as well.