An endophyte is a microorganism that spends most of its life cycle inter- or intra-cellularily of the host organism without causing its disease. As a result of the high frequency of endophytes in plants, it is virtually impossible to isolate tissue or cell explants free from contaminants. Consequently, preculture (i.e. ??stage 0?) is necessary before disinfecting and stabilisation of in vitro cultures, to eliminate explants that are sources of persistent contamination. Particularly dangerous are latent bacterial contaminants, which initially do not cause any symptoms and are propagated with plant material. Their presence becomes conspicuous after the passage to a sucrose-free medium or after transplantation to the soil. This paper reviews the modern methods of treatment that are recommended or have already been widely used to control viruses, phytoplasmas, bacteria, yeast and other fungi associated with tissues of propagated plants.