Abstract Simple inversion of a DNA fragment simultaneously alters both trp1 and his3 expression in yeast even though the inversion break points map more than 300 base-pairs from either structural gene. In the inverted configuration, a his3 null allele is abnormally expressed and the wild-type trp1 allele is not expressed. These unexpected phenotypes are probably not caused directly by readthrough transcription from nearby promoters. Thus, it is important to consider potential position effects when interpreting the phenotypes of alleles produced by chromosomal rearrangement, as sequences located more than 300 base-pairs from the structural gene can play a major role.