Despite significant progress, the general functional and evolutionary significance of the untranslated regions (UTRs) of eukaryotic transcripts remain mysterious. Particularly mysterious is the common occurrence of spliceosomal introns in transcript UTRs because UTR splicing is not necessary for restoration of transcript coding sequence. In general, it is not known to what extent such splicing performs an important function or merely represents spliceosomal "noise." We conducted the first analysis of evolutionary conservation of UTR splicing. Among 4 species from Cryptococcus neoformans species complex, we find high levels of conservation of UTR intron boundary sequences, strongly suggesting that UTR intron splicing is conserved by purifying selection. We estimate that 50-90% of splice boundaries are maintained by selection. Donor site sequences are more highly conserved than acceptor sequences, and splicing boundaries are more conserved in 5' UTRs than in 3' UTRs. In addition, we report a variety of differences between patterns of UTR splicing in Cryptococcus and corresponding patterns in animals and plants. These results focus attention on the functional roles of eukaryotic UTRs and deepen the mystery of UTR intron splicing.