The use of molecular techniques in cytopathology has become an accepted and billable practice for certain applications. Other applications still are in the developmental or experimental stages but may soon be clinically useful. The current study provides a review of these techniques including molecular detection of clonality, in situ hybridization, loss of heterozygosity, and single base mutation detection. A number of new molecular techniques recently have been described that may have a dramatic impact on diagnostic pathology. These techniques, in situ detection of single base mutations and microarray technology, are introduced and discussed in the context of potential applications to cytopathology in the future.