In an experimental mouse model infected with ZIKV, global transcriptome analyses (RNA-sequencing) identified genes related to cytokine production and cytokine response; several genes related to cell proliferation, differentiation, and migration were downregulated; and most of the microcephaly-related genes were downregulated (ASPM, CASC5, CENPF, MCPH1, RBBP8, STIL, and TBR2). Here, STIL is linked to microcephaly.