There are several reports of a closer-than-random colocalization of homologous 
chromosomes in the vegetative nuclei of diploid budding yeast. Here, we studied 
by fluorescence in situ hybridization (FISH) the nuclear distribution of 
chromosomes and found a slight tendency toward closer proximity between 
homologous (allelic) loci than between any nonhomologous chromosomal regions. We 
show that most of this preferential association is not due to vegetative (also 
known as somatic) pairing but is caused by the polar orientation of interphase 
chromosomes (Rabl orientation). We quantified the occasional loss of detectable 
fluorescence signals that is inherent to the FISH method. Signal loss leads to 
the occurrence of a single signal that may be misinterpreted as the close 
association of two homologous chromosomal sites. The nuclear distribution of 
homologous loci, when corrected for the influence of nuclear architecture and 
methodological faults, was not different or was only marginally different from a 
random relative positioning as predicted by computer simulation. We discuss here 
several possibilities for the residual homologous proximity that do not invoke 
homology-dependent vegetative pairing, and we conclude that, in diploid budding 
yeast, constitutive vegetative pairing is a negligible factor for the 
organization of the interphase nucleus.