Genes showing similar expression patterns are often clustered along the genome. We demonstrate the existence of correlated expression across multiple scales, from neighboring genes to chromosomal domains that span tens of megabases and, in some cases, entire chromosomes. Domains may be positively or negative correlated with other domains, within and between chromosomes. We provide evidence that long-range expression domains are associated with gene density, which in turn is related to physical organization of the chromosome within the nucleus. Changes in gene expression patterns between healthy and diseased tissue samples suggest that chromosome territory reorganization may play role in some human diseases.