A potentially significant problem following bisulfite treatment is incomplete desulfonation of pyrimidine residues due to inadequate alkalization of the solution. This may inhibit some DNA polymerases, rendering subsequent PCR difficult. However, this situation can be avoided by monitoring the pH of the solution to ensure that desulfonation will be complete.
A final concern is that bisulfite treatment greatly reduces the level of complexity in the sample, which can be problematic if multiple PCR reactions are to be performed (2006). Primer design is more difficult, and inappropriate cross-hybridization is more frequent.