Endophytic fungi colonize plant tissues without causing any manifestations or disease in the host plants. These fungi have been isolated from various plants living in a wide variety of habitats. It is estimated that all plants are colonized by one or more species of endophytic fungus that confer one or more advantages to the host plant due to their ability to synthesize bioactive molecules with applications in agriculture, biotechnology, and medicine. This chapter outlines general methods of collection and processing fungal endophytes from terrestrial plants.