Non-synonymous coding mutations in a gene change the resulting protein, no matter where it is expressed, but the effects of cis-regulatory mutations could be spatially or temporally limited - a phenomenon termed limited pleiotropy. Here, we report the genome-wide occurrence of limited pleiotropy of cis-regulatory mutations in barley (Hordeum vulgare L.) using Affymetrix analysis of 22,840 genes in a population of 139 doubled haploid lines derived from a cross between the cultivars Steptoe (St) and Morex (Mx). We identified robust cis-acting expression regulators that segregate as major genes in two successive ontogenetic stages: germinating embryo tissues and seedling leaves from the embryonic axis. We show that these polymorphisms may be consistent in both tissues or may cause a dramatic change in transcript abundance in one tissue but not in another. We also show that the parental allele that increases expression can vary with the tissue, suggesting nucleotide polymorphism in enhancer sequences. Because of the limited pleiotropy of cis-regulating mutations, the number of cis expression quantitative trait loci (cis-eQTLs) discovered by 'genetical genomics' is strongly affected by the particular tissue or developmental stage studied. Given that limited pleiotropy is a common feature of cis-regulatory mutations in barley, we predict that the phenomenon would be relevant to developmental and/or tissue-specific interactions across wide taxonomic boundaries in both plants and animals.