Immunological detection of low molecular weight toxins, such as deoxynivalenol using single-chain antibody fragment (scFv), is a potentially novel and safe method of diagnosing fungal infection and food contamination. To develop a deoxynivalenol detection procedure based on scFv, deoxynivalenol was first conjugated to horseradish peroxidase (HRP) for immunoassay. Deoxynivalenol was initially activated using N-[p-maleimidophenyl] isocyanate and subsequently conjugated to S-acetyl thioglycolic acid N-hydroxysuccinimide-activated HRP. Sodium dodecylsulphate polyacrylamide gel electrophoresis and enzyme-linked immunosorbent assay (ELISA) analysis confirmed covalent attachment of deoxynivalenol to HRP successfully. Competitive direct-ELISA based on antideoxynivalenol scFv was used to detect deoxynivalenol in spiked and natural contaminated wheat samples, and the results showed that scFv is applicable in deoxynivalenol detection of contaminated wheat samples. This work confirms that sensitive and specific scFv against fungal toxins can be applicable in diagnosis of fungal infection.