Understanding how genetic variation is maintained begins with a comprehensive description of what types of genetic variation exist, the extent and magnitude of the variation, and patterns discernable in that variation. However, such studies have focused primarily on DNA sequence data and have ignored genetic variation at other hierarchical levels of genetic information. Microarray technology permits an examination of genetic variation at the level of mRNA abundance. Utilizing a round-robin design, we present a quantitative description of variation in mRNA abundance in terms of GCA (general combining ability or additive variance). We test whether genes significant for GCA are randomly distributed across chromosomes and use a nonparametric approach to demonstrate that the magnitude of the variation is not random for GCA. We find that there is a paucity of genes significant for GCA on the X relative to the autosomes. The overall magnitude of the effects for GCA on the X tends to be lower than that on the autosomes and is contributed by rare alleles of larger effect. Due to male hemizygosity, GCA for X-linked phenotypes must be due to trans-acting factors, while GCA for autosomal phenotypes may be due to cis- or trans-acting factors. The contrast in the amount of variation between the X and the autosomes suggests that both cis and trans factors contribute to variation for expression in D. simulans with the preponderance of effects being trans. This nonrandom patterning of genetic variation in gene expression data with respect to chromosomal context may be due to hemizygosity in the male.