Systematic desentisation has been criticised for not being appropriate for all phobias.
The whole treatment is based on the idea of counter-conditioning and some phobias such as specific phobias like claustrophobia aren't 'learnt' or conditioned.
Seligman stated that some phobias may occur due to biological preparedness which means they occur due to survival instincts like fear of snakes.
Therefore systematic desentisation could not be used to treat these types of phobias which limits its effectiveness.