Early postnatal infection with human cytomegalovirus (hCMV) may contribute to an adverse cognitive outcome in early preterm-born children (PT). We here set out to explore whether long-term neurobiological consequences of such an infection are detectable using fMRI in children and adolescents who were born very preterm and who either did (PThCMV+) or did not (PThCMV−) suffer from an early postnatal hCMV-infection, when compared with typically developing healthy control (HC) subjects. Overall, data from 71 children and adolescents could be included, 34 PT (of which 15 were PT hCMV+ and 19 were PT hCMV−) and 37 HC. Using a recently established “dual use” fMRI task, we investigated language and visuospatial functions. There were significant activation differences in the left hippocampus (PT > HC and PThCMV+ > HC), and in the right anterior cingulate cortex (PThCMV− > PThCMV+) when performing the language task. Surprisingly, only a small region in the occipital cortex showed a significant activation difference (HC > PT HCMV−) when performing the visuospatial task. Targeted analyses revealed differences in gray matter volume, but not density, in several brain regions. Our results suggest that long-term neurobiological consequences of an early postnatal hCMV infection are detectable even in older children and adolescents formerly born very preterm, compatible with a higher effort when performing a cognitive task. This suggests that measures to prevent such an infection are warranted. Furthermore, an interrelation of brain structure and function was detected that may constitute a severe confound when using fMRI to compare structurally differing groups. Hum Brain Mapp 35:2594–2606, 2014. © 2013 Wiley Periodicals, Inc.