MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects. The system allows specification of constraints of the location and distances between the primers in a pair. For instance, primers in coding, non-coding, exon/intron-spanning regions might be selected. Medusa applies these constraints as a filter to primers predicted by three external programs, and displays the resulting primer pairs graphically in the Blixem (Sonnhammer and Durbin, COMPUT: Appl. Biosci. 10, 301-307, 1994, http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html) viewer.