Brain cognition relies on synapses,the basic functional units in neuronal circuits.Directly visualizing the organization of molecular machineries inside specific synapses is highly desirable but challenging due to synaptic heterogeneity.Here,we combined cryo electron tomography(cryoET)with correlative light microscopy to identify specific synapses in intact hippocampal neurons and to analyze their three-dimensional ultrastructure.This approach allowed us to visualize the in situ organization of synaptic organelles and macromolecules in their native states.Quantitative measurements revealed two distinct profiles of the postsynaptic density for excitatory and inhibitory synapses.“Frisbee-shaped” ellipsoidal vesicles were observed in both synaptic types,with more in inhibitory synapses.Furthermore,high-resolution cryoET analysis of individual synapses identified populations of membrane proteins,with sizes similar to those of glutamate and GABA receptors.These results demonstrate the applicability and potential of correlative cryo light and electron microscopy in the understanding of heterogeneous ultrastructures underlying distinct synaptic functions.