A QTL mapping study in Arabidopsis thaliana reveals both the extent to which stochastic noise in gene expression is genetically controlled and the genomic distribution of the variants. The authors mapped polymorphisms underlying stochastic noise in the accumulation of a class of plant defence metabolites and in related transcripts, and they identified noise QTLs that specifically influence transcript or metabolite levels. Similarly, at the whole-transcriptome level, the authors identified QTLs that are responsible for genome-wide stochastic noise that were distinct from those controlling average transcript levels.