Resistance of elms ( Ulmus spp.) to the pathogenic fungus Ophiostoma novo-ulmi Brasier depends on chemical and anatomical factors that confine the spread of the pathogen in the vascular system of the host. This study focused on detecting chemical differences in 4-year-old Ulmus minor Mill. seedlings before and after inoculation with a virulent O. novo-ulmi isolate. According to symptom development over 60 days, the trees were divided into resistant (0–33% wilting) and susceptible (67–100% wilting) groups. Histochemical tests and Fourier transform-infrared (FT-IR) spectroscopy analysis were performed on transverse sections of 2-year-old twigs, 2 days before and 40 days after inoculation. Although histochemical tests did not clearly discriminate susceptible from resistant elms, chemical differences between resistant, susceptible and control trees were detected by FT-IR. The average spectrum for resistant tree samples had higher absorbance peaks than the spectra from the susceptible and control samples, indicating increased formation of lignin and suberin. The roles of lignin and suberin in the resistance of the elms against O. novo-ulmi and the usefulness and sensitivity of the FT-IR technique for analyzing metabolic changes caused by pathogens in plants are discussed.