Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these questions. Our results indicate that open reading frames (ORFs) with similar G+C contents at silent codon positions are significantly clustered on chromosomes. This clustering can be explained by very short range correlations of silent-site G+C contents at neighboring ORFs. ORFs of high silent-site G+C content are disproportionately concentrated on shorter chromosomes, which causes a negative relationship between chromosome length and G+C content. Contrary to previous reports, there is no correlation between gene density and silent-site G+C content in yeast. Chromosome III is atypical in many regards, and possible reasons for this are discussed.