This database contains the connectivity matrices of the resting-state functional MRI scans that were collected in two databases of the Human Connectome Project, Young Adult and Aging. These matrices contain the functional connectivity between brain regions (here, several different brain atlases were used, leading to several different connectivity matrices for each subject). The connectivity matrices are symmetrical n x n matrices. Here, n indicates the number of regions present in the atlas, and any number ni,j in the matrix is generated by calculating a simple Pearson correlation coefficient between the functional time series that describe the functional activation of regions i and j throughout the resting-state functional scan. The matrices presented in this database are present as .pconn.nii files (which can be handled using software like wb_command) or as .txt file. A full explanation of the database and the brain atlases used here, as well as all the scripts used to generate these connectivity matrices can be found on the GitHub page of this project: floristijhuis/HCP-rfMRI-repository (github.com).