Laboratory mouse models represent a powerful tool to elucidate the biological foundations of disease, but translation to and from human studies rely upon valid cross-species measures. Resting-state functional connectivity (rsFC) represents a promising translational probe of brain function; however, no convincing demonstration of the presence of distributed, bilateral rsFC networks in the mouse brain has yet been reported. Here we used blood oxygen level dependent (BOLD) and cerebral blood volume (CBV) weighted fMRI to demonstrate the presence of robust and reproducible resting-state networks in the mouse brain. Independent-component analysis (ICA) revealed inter-hemispheric homotopic rsFC networks encompassing several established neuro-anatomical systems of the mouse brain, including limbic, motor and parietal cortex, striatum, thalamus and hippocampus. BOLD and CBV contrast produced consistent networks, with the latter exhibiting a superior anatomical preservation of brain regions close to air-tissue interfaces (e.g. ventral hippocampus). Seed-based analysis confirmed the inter-hemispheric specificity of the correlations observed with ICA and highlighted the presence of distributed antero-posterior networks anatomically homologous to the human salience network (SN) and default-mode network (DMN). Consistent with rsFC investigations in humans, BOLD and CBV-weighted fMRI signals in the DMN-like network exhibited spontaneous anti-correlation with neighbouring fronto-parietal areas. These findings demonstrate the presence of robust distributed intrinsic functional connectivity networks in the mouse brain, and pave the way for the application of rsFC readouts in transgenic models to investigate the biological underpinnings of spontaneous BOLD fMRI fluctuations and their derangement in pathological states.