Molecular fingerprint indices are derived from Jacobi expansion of molecular electron density in a ball. Electron density computed in the linear combination of atomic orbitals framework, at any computational level, is expanded in terms of suitable Jacobi polynomials times regular spherical harmonics. The procedure is applicable to calculations with either Gaussian or Slater-type orbitals. A very efficient algorithm previously reported for Canterakis–Zernike expansions is shown to be also applicable for this type of expansions. The procedure has been implemented in the DAMQT suite for the analysis of electron density, which facilitates the application to densities obtained with standard packages for molecular structure calculations. Fingerprints derived from Jacobi expansions are compared with other derived from Canterakis–Zernike expansions in some pharmacological molecules.