Two adjacent polygalacturonase-inhibiting protein (PGIP) genes were characterized from the model legume Medicago truncatula. MtPGIP1 and MtPGIP2 were isolated from a single bacterial artificial chromosome clone identified from library-screening with cDNA probes. Ten and nine characteristic stretches of leucine-rich repeats, respectively, were identified from the predicted MtPGIP1 and MtPGIP2, showing 58% sequence identity at the amino acid level. These MtPGIP genes are likely present as a small gene family. Transcripts encoding MtPGIP1 were expressed highly in the flowers and at low levels in the roots and stems, whereas those encoding MtPGIP2 were not detected in any untreated organs. Inoculation of the A truncatula cultivar 'Jemalong' with the pathogenic fungus Colletotrichurn trifolh induced a hypersensitive response and the expression of both genes. The two genes were also expressed in response to the application of jasmonic acid, although mechanical wounding induced only MtPGIP1 and salicylic acid induced neither. Abiotic stresses, such as high-salt, cold, or drought, induced the expression of MtPGIP1, whereas low-temperature stress induced MtPGIP2 only. Consistent with these observations, sequence elements specific to plant defense and stress responses were identified, in varying numbers, from the putative promoter regions of the two genes. Furthermore, supportive of their putative functional roles, bacterially expressed recombinant MtPGIP1 and MtPGIP2 inhibited fungal polygalacturonase activity. Therefore, these results suggest that MtPGIP1 and MtPGIP2, copies that presumably arose from duplication, are regulated by separate signaling pathways and likely play roles in response to pathogenic and environmental stresses.