tRNA-splicing endonuclease from the yeast Saccharomyces cerevisiae was purified to homogeneity greater than 5000-fold over a crude Triton X-100 extract of yeast total membranes, with 5% overall yield. This nuclear enzyme has the unusual heterotrimeric subunit structure alpha beta gamma (alpha = 31 kDa, beta = 42 kDa, and gamma = 51 kDa), as determined by sodium dodecyl sulfate gel electrophoresis, and has a molecular mass close to the sum of the three subunits, as determined by gel filtration of the native enzyme. From the purification, we estimate that there are approximately 100 molecules of endonuclease/cell.