Endophytic fungi are a taxonomically and ecologically heterogenous group of organisms, mainly belonging to the Ascomycotina and Deuteromycotina. The isolation methods affect the species composition of the endophyte assemblage in a given host. The number of endophyte taxa isolated from a host species is usually large; however, only few, normally host specific species or strains are dominant. Endophyte assemblages are specific at the host species level, but species composition and frequencies are significantly affected by site-specific conditions. Moreover, the relative importance and number of endophytic species vary among individuals within sites. In some cases, each individual could be considered a separate ecosystem. In general, however, 40 individuals with 30 to 40 sampling units per organ and individual should be enough to detect 80% of taxa present in a given host at one site. Endophytes usually produce the enzymes necessary for the colonization of plant tissues. Substrate utilization studies and isozyme analysis have demonstrated that most endophytes are able to utilize most plant cell components. The production of growth promoting factors and of metabolites useful in the pharmaceutical and agricultural industry is widespread among endophytic fungi. The usefulness of endophytes in agricultural and pharmaceutical research is briefly discussed.