A cathepsin L protease full-length cDNA (named Mi-cpl-1) was characterised from infective second-stage juveniles of the root-knot nematode Meloidogyne incognita by SL1-primed PCR and 3′ rapid amplification of cDNA ends (3′-RACE). A single open reading frame was identified, encoding a putative 383-amino acid protein predicted to contain a putative N-terminal short secretion signal peptide, which suggests that Mi-CPL-1 should function as an extracellular protein. The putative mature enzyme included several conserved amino acid residues/motives, among which the typical catalytic triad of the active site. In situ mRNA hybridization analyses showed that transcripts of Mi-cpl-1 accumulated specifically in the intestinal cells of specimens, which suggests that the protein could be involved in the digestive processes of the nematode. However, expression of Mi-cpl-1 was shown to occur exclusively in the developmental stages which are in close interaction with the root tissues (i.e. second-stage juveniles and females). This may indicate that some function of the cathepsin L cysteine protease in M. incognita is more directly related to the parasitic aspects of the plant-nematode relationship, e.g. pathogenicity and/or evasion of primary host plant defence systems.