It has been known for almost a decade and a half that in trypanosomes all mRNAs are trans-spliced by addition to the 5′ end of the spliced leader (SL) sequence. During the same time period the conviction developed that classical cis-splicing introns are not present in the trypanosome genome and that the trypanosome gene arrangement is highly compact with small intergenic regions separating one gene from the next. We have now discovered that these tenets are no longer true. Poly(A) polymerase (PAP) genes in Trypanosoma brucei and Trypanosoma cruzi are split by intervening sequences of 653 and 302 nt, respectively. The intervening sequences occur at identical positions in both organisms and obey the GT/AG rule of cis-splicing introns. PAP mRNAs are trans-spliced at the very 5′ end as well as internally at the 3′ splice site of the intervening sequence. Interestingly, 11 nucleotide positions past the actual 5′ splice site are conserved between the T. brucei and T. cruzi introns. Point mutations in these conserved positions, as well as in the AG dinucleotide of the 3′ splice site, abolish intron removal in vivo. Our results, together with the recent discovery of cis-splicing introns in Euglena gracilis, suggest that both trans- and cis-splicing are ancient acquisitions of the eukaryotic cell.