Determining the number of synapses that are present in different brain regions is crucial to understand brain connectivity as a whole. Membrane-associated guanylate kinases (MAGUKs) are a family of scaffolding proteins that are expressed in excitatory glutamatergic synapses. We used genetic labeling of two of these proteins (PSD95 and SAP102), and Spinning Disc confocal Microscopy (SDM), to estimate the number of fluorescent puncta in the CA1 area of the hippocampus. We also used FIB-SeM, a three-dimensional electron microscopy technique, to calculate the actual numbers of synapses in the same area. We then estimated the ratio between the three-dimensional densities obtained with FIB-SEM (synapses/µm 3) and the bi-dimensional densities obtained with SDM (puncta/100 µm 2). Given that it is impractical to use FIB-SEM brain-wide, we used previously available SDM data from other brain regions and we applied this ratio as a conversion factor to estimate the minimum density of synapses in those regions. We found the highest densities of synapses in the isocortex, olfactory areas, hippocampal formation and cortical subplate. Low densities were found in the pallidum, hypothalamus, brainstem and cerebellum. finally, the striatum and thalamus showed a wide range of synapse densities. Determining the number of synapses that are present in different brain regions is crucial to understand brain connectivity as a whole. Synapses can be identified with several methods, including genetic labeling of synaptic scaffolding proteins and electron microscopy (EM). Membrane-associated guanylate kinases (MAGUKs) are a family of scaffolding proteins that participate in the regulation of cell polarity, cell adhesion and synaptic signal transduction 1-3. PSD95 and SAP102 belong to the MAGUK family and are expressed in the postsynaptic density (PSD) of excitatory glutamatergic synapses 4-12 , where they contribute to the recruitment and retention of glutamate receptors 13-15. Genetic labeling of the endogenous PSD95 and SAP102 postsynaptic proteins and imaging using Spinning Disk confocal Microsocpy (SDM) have been proven to be useful for the characterization of synapse diversity in all brain regions of the mouse. SDM is a rapid method that allows the imaging of entire brain sections, so the simultaneous visualization of millions of synapses is made possible, obtaining bi-dimensional densities of fluorescent puncta per surface area (puncta/100 µm 2) 16. Previous attempts have been made to calculate the density of synapses in the brain using EM. This technique allows the identification of individual synapses, although it is restricted to much smaller fields of view. Furthermore, most of these EM studies apply stereological techniques to a limited number of EM sections. Although stereology is a proven valuable method for object counting, the total number of synapses is an estimation which is subject to several technical limitations [see 17 for a review]. In the present study, we use Focused Ion Beam