The number of molecular imaging studies in the field of brain connectivity is steadily increasing.Molecular imaging is not yet widely used by the MRI-predominant neuroimaging community as tool of choice for studying brain connectomics.Because chemical synapses are essential to signal transduction, targeting the molecular level of brain communication is indispensable for our understanding of the brain connectome.PET as major molecular imaging tool provides various established markers of neural activity, neurotransmitter systems, and proteinopathies.Integration of connectomes produced with different neurophysiological methods, including molecular imaging, might be key for advancing the field of neuroscience. In the past two decades brain connectomics has evolved into a major concept in neuroscience. However, the current perspective on brain connectivity and how it underpins brain function relies mainly on the hemodynamic signal of functional magnetic resonance imaging (MRI). Molecular imaging provides unique information inaccessible to MRI-based and electrophysiological techniques. Thus, positron emission tomography (PET) has been successfully applied to measure neural activity, neurotransmission, and proteinopathies in normal and pathological cognition. Here, we position molecular imaging within the brain connectivity framework from the perspective of timeliness, validity, reproducibility, and resolution. We encourage the neuroscientific community to take an integrative approach whereby MRI-based, electrophysiological techniques, and molecular imaging contribute to our understanding of the brain connectome.