In almost all species of termites (Isoptera), there is a distinct soldier caste that specifically plays a defensive role. In many termite species, soldiers defend the colony mechanically with their mandibles. However, nasute soldiers in the subfamily Nasutitermitinae (family Termitidae) use chemical defense, projecting repellent substances synthesized in frontal glands present within the head. As the nasute soldiers always synthesize a large amount of defensive secretion after soldier differentiation, many genes involved in the biosynthesis of this secretion should always be expressed. To identify and isolate the genes related to chemical defense, we compared the gene expression profiles in the heads of soldiers and workers in a nasute termite, Nasutitermes takasagoensis, by fluorescent differential display (FDD). The ratio of soldier-specific bands was relatively high (6.9%) compared with that of mandibulate soldiers. The distinct soldier-specific bands were excised, and 21 sequences of cDNA fragments were cloned. Of these, only seven candidates had homologous sequences to known genes (eukaryotic initiation factor 4A-I, 3β-hydroxysteroid dehydrogenase/isomerase family, alkaline phosphatase homolog, GTP-binding protein, ribosomal protein S13, family 4 cytochrome P450 and an unknown protein). To exclude false positives of the FDD analysis, semi-quantitative reverse transcription–polymerase chain reaction was carried out for all 21 candidates. Only eight gene candidates (only one showed sequence homology) showed significantly higher expression levels in soldiers than in workers.