The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related genes. Here, we describe new, freely available software called Common Introns Within Orthologous Genes (CIWOG), available at http://ciwog.gdcb.iastate.edu/, which detects common introns in protein-coding genes based on position and sequence conservation in the corresponding protein alignments. CIWOG provides dynamic web displays that facilitate detailed intron studies within orthologous genes. User-supplied options control how introns are clustered into sets of common introns. CIWOG also identifies special classes of introns, in particular those with GC- or U12-type donor sites, which enables analyses of these introns in relation to their counterparts in the other genes in orthologous groups. The software is demonstrated with application to a comprehensive study of eight plant transcriptomes. Three specific examples are discussed: intron class conversion from GT- to GC-donor-type introns in monocots, plant U12-type intron conservation and a global analysis of intron evolution across the eight plant species.