The output of the retina is carried by retinal ganglion cells (RGCs) along parallel functional pathways to multiple areas distributed across the vertebrate brain. The functional organization of the synaptic connections between RGCs and their postsynaptic target neurons is largely unknown. Here, we discovered that high-density Neuropixels probes allow the measurement of large populations of RGC axons where they form synaptic contacts, in vivo. The electrophysiological signature of RGC afferent inputs is made of a triphasic waveform composed of the axonal action potential, the axonal terminal response and, finally, the corresponding responses from the synaptically connected dendrites. The signal is spread across multiple recording sites, capturing the axonal synaptic contact field of individual RGCs in vivo. Consequently, midbrain neurons can be recorded simultaneously with their presynaptic RGC inputs, at large scales reaching up to 200 functionally connected pairs in individual recordings. Furthermore, we confirmed that these large-scale paired recording are possible in both the mammalian superior colliculus (mouse, Mus musculus) and the avian optic tectum (zebra finch, Taeniopygia guttata). Using our novel approach to study the spatial organization of retinal axons within the midbrain, we discovered that retinal mosaics are mapped onto the midbrain isomorphically with single cell precision. Functionally, we show that single RGC axons connect to their target neurons with strong and specific connections, i.e., a limited functional convergence and log-normally distributed connection strength. Overall, our results show that high-density electrodes can capture multiple neuronal compartments simultaneously in vivo, including afferent axons and their synaptically evoked dendritic responses as well as somatic activity of local neurons; permitting large-scale paired recordings between brain regions. In addition, we conclude that the retinotectal connectivity follows a common organizing principle in mammals and birds that provides a precise and reliable representation of the visual world to neurons in the midbrain.