Background: In animals, the moss Physcomitrella patens and the pollen of Arabidopsis thaliana, highlyexpressed genes have shorter introns than weakly expressed genes. A popular explanation for thisis selection for transcription efficiency, which includes two sub-hypotheses: to minimize theenergetic cost or to minimize the time cost.Results: In an individual human, different organs may differ up to hundreds of times in cell number(for example, a liver versus a hypothalamus). Considered at the individual level, a gene specificallyexpressed in a large organ is actually transcribed tens or hundreds of times more than a gene witha similar expression level (a measure of mRNA abundance per cell) specifically expressed in a smallorgan. According to the energetic cost hypothesis, the former should have shorter introns than thelatter. However, in humans and mice we have not found significant differences in intron lengthbetween large-tissue/organ-specific genes and small-tissue/organ-specific genes with similarexpression levels. Qualitative estimation shows that the deleterious effect (that is, the energeticburden) of long introns in highly expressed genes is too negligible to be efficiently selected againstin mammals. Conclusion: The short introns in highly expressed genes should not be attributed to energyconstraint. We evaluated evidence for the time cost hypothesis and other alternatives.