Different services are widely used for the modelling of secondary structure of internal transcribed spacers, ITS1 and ITS2, fragments of eucaryotic nuclear ribosomal gene cluster. Results of these analyses are presented in many phylogenetic studies. Stability of RNA structure depends on folding conditions (ionic strength, temperature, pressure, pH). But often the information about thermodynamic parameters is missed. Which conditions are better for standardizing of in silico ITS structure analysis?