For this dataset synapses have been identified, segmented and quantified in the deep part of the pyramidal layer, the stratum oriens and the stratum lacunosum-moleculare of the CA1 field of the human hippocampus with 3D electron microscopy (FIB-SEM). 5 human autopsies have been used to achieve a total of 15 valid images stacks (3 stacks per case) per investigated region. Data include the number and density per volume of asymmetric and symmetric synapses, their sizes and their 3D spatial position. The distribution of their post-synaptic targets has also been determined. This dataset contains additional data related to the dataset by Dominguez-Alvaro et al. (2020; doi: 10.25493/6HRE-F2Y). Experiments were performed identically, and the data from these two dataset can be used in combination.