From the approximately 5000 open reading frames presently identified by systematic sequencing of the yeast genome, 100 Saccharomyces cerevisiae transport proteins belonging to the major facilitator superfamily (MFS), were assigned to 17 families on the basis of extensive database searches and binary comparisons. These families include multidrug resistance proteins and transport proteins for sugars, amino acids, uracil/allantoin, allantoate, phosphate, purine/cytosine, proteins, peptides, potassium, sulfate, and urea. Four new families of unknown function have been identified. For the sugar and amino acid transport proteins, alignments were made and phylogenetic trees were constructed allowing the identification of several clusters of proteins presumably exhibiting similar transport functions.