To ascertain the effect of relaxation of selection on global gene expression, Caenorhabditis elegans mutation accumulation (MA) lines were propagated under varying degrees of efficiency of selection determined by their different population sizes (N = 1, 10 and 100). Both the mutational variance (Vm), and the residual variance (Vr) were greatest in MA lines with the lowest efficiency of natural selection. The results suggest that gene expression is under strong balancing selection. Furthermore, mutations resulting in increased transcriptional noise or sensitivity to microenvironmental variation accumulate most under extreme genetic drift. In contrast, the Vm/Vr ratio was lowest in the N = 1 lines. Chromatin domains associated with broad gene silencing and active transcription exhibited the greatest and the smallest increase in transcriptional variation, respectively. Furthermore, the preponderance of overexpressed genes was especially pronounced in mitochondrial respiration, stress response, and immune system pathways, especially in low fitness N = 1 lines