The fungus Piriformospora indica promotes growth and seed production of Arabidopsis thaliana plants, very similar to what has been observed for other plant species. Using molecular tools and mutant screens, two leucine-rich repeat proteins, LRR1 and LRR2, were identified which are involved in the recognition of the two symbiotic partners. The mRNA for LRR1 is transiently upregulated in A. thaliana roots co-cultivated with P. indica. Mutants which do not respond to P. indica do not show this upregulation. LRR1 is an atypical receptor kinase located in the plasma membrane. The protein is present in Triton X-100 insoluble plasma membrane microdomains. A mutant with a lesion in another leucine-rich repeat protein, LRR2, also fails to accumulate LRR1 in Triton X-100 insoluble plasma membrane microdomains. The requirement of LRR1 for the symbiotic interaction is unclear, because no functional knock out line is available. Two mutants with lesions in LRR2 were characterized. Both of them fail to respond to P. indica with regard to growth promotion and enhanced seed production. LRR2 appears to be loosely associated with Triton X-100 insoluble plasma membrane microdomains and might be located in the endoplasmatic reticulum. Triton X-100 insoluble plasma membrane microdomains were isolated from A. thaliana and the protein composition of this fraction was determined by mass spectrometry. 34 proteins mainly related to signalling processes are present in this preparation, including seven leucine-rich repeat proteins. Two of them are LRR1 and LRR2. DMI1 is an essential protein for mycorrhiza formation in legumes. Inactivation of the only homologous gene in A. thaliana, a gene that is exclusively expressed in roots does not affect growth promotion and enhanced seed production in A. thaliana in response to P. indica. Thus, the endophytic interaction between P. indica and A. thaliana appears to differ from mycorrhiza in Legumes. The interaction between A. thaliana and P. indica is accompanied by the modification of a plasma membrane-localized MATH protein (Peskan-Berghöfer et al. 2004). This protein modification does not occur in an Arabidopsis mutant, which does not respond to P. indica. At present the function of MATH proteins is still unclear; however, the modular organization and domain structure of MATH proteins suggest that they may be involved in protein degradation or protein/peptide cleavage. This homeodomain transcription factor BHL1 responds to the fungus and binds to promoter regions of the P. indica responsive Nia2, SEX1 and 2-nitropropane dioxygenase genes in tobacco (Sherameti et al. 2005). Inactivation of the BHL1 gene in A. thaliana completely abolished the growth promotion and enhanced seed production.