We investigated soybean lectin gene structure and expression in a genetic line that accumulates normal levels of seed lectin (Le+ line) and in a mutant line that produces no detectable seed lectin (Le- line). We found that the nuclear and cytoplasmic lectin RNA levels in Le- embryos are approximately 0.01% of those in Le+ embryos. Runoff transcription experiments with isolated nuclei showed that the reduced RNA levels are caused by decreased lectin gene transcription. Each genetic line contains two lectin genes, L1 and L2. L1 encodes seed lectin, while the function of L2 is unknown. We found that a 3.4 kb DNA segment, consisting of repeated sequences, has been inserted into the L1 gene of the Le- line. We conclude that this insertion results in reduced transcription of the mutant L1 gene, and leads to the lectinless phenotype.