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Background: The recently sequenced genome of the filamentous fungus Ashbya gossypiirevealed remarkable similarities to that of the budding yeast Saccharomyces cerevisiaeboth at the level of homology and synteny (conservation of gene order). Thus, it became possible to reinvestigate the S. cerevisiaegenome in the syntenic regions leading to an improved annotation. Results: We have identified 23 novel S. cerevisiaeopen reading frames (ORFs) as syntenic homologs of A. gossypiigenes; for all but one, homologs are present in other eukaryotes including humans. Other comparisons identified 13 overlooked introns and suggested 69 potential sequence corrections resulting in ORF extensions or ORF fusions with improved homology to the syntenic A. gossypiihomologs. Of the proposed corrections, 25 were tested and confirmed by resequencing. In addition, homologs of nearly 1,000 S. cerevisiaeORFs, presently annotated as hypothetical, were found in A. gossypiiat syntenic positions and can therefore be considered as authentic genes. Finally, we suggest that over 400 S. cerevisiaeORFs that overlap other ORFs in S. cerevisiaeand for which no homolog can be detected in A. gossypiishould be regarded as spurious. Conclusions: Although, the S. cerevisiaegenome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, we have shown that it still benefits substantially from comparison to the completed sequence and syntenic gene map of A. gossypii, an evolutionarily related fungus. This type of approach will strongly support the annotation of more complex genomes such as the human and murine genomes.