The physical effects of disease induced by Citrus tristeza virus (CTV) on its citrus host have long been known, but not how disease is induced either by the virus, or its effects on the host at the genetic level. In this study we aimed to examine the latter, by deliberate inoculation of Citrus macrophylla with a mutant T36-based infectious clone known to induce stem pitting and other growth abnormalities. The microRNA populations of disease-expressing plants were compared with plants infected with asymptomatic, wild-type T36, and with un-inoculated controls. We found that while virus infection induced change in expression of a large number of miRNAs, the onset of disease correlated with the downregulation of miR164, a miRNA associated with vascular differentiation. This is the first evidence of specific host miRNAs associated with the induction of a CTV disease syndrome.