Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations. It comprises efficient and well parallelized programs for standard computational chemistry applications, such as DFT with a large choice of functionals, as well as state-of-the art high-level coupled-cluster and multi-reference wave function methods. Electronically excited states can be treated using MCSCF/CASSCF, CASPT2, MRCI, or FCI methods, or by response methods such as TDDFT, CC2, and EOM-CCSD. There are many modules for computing molecular properties, geometry optimization, calculation of harmonic and anharmonic vibrational frequencies, and further wave function analysis. Analytical energy gradients are available for DFT, HF, MP2, CCSD, DCSD, QCISD, QCISD(T), CASSCF, and CASPT2. Density fitting (DF or RI) approximations can speed up DFT and MP2 calculations with large basis sets by orders of magnitude, and explicitly correlated methods [MP2-F12, CCSD(T)-F12, CASPT2-F12, MRCI-F12] minimize basis set incompleteness errors to yield near CBS quality results with triple-zeta basis sets. Combined with local approximations and efficient parallelizations, high-level methods [LMP2-F12, LCCSD(T)-F12] can be be applied to large molecules of chemical interest, yielding unprecedented accuracy. Furthermore, WF-in-DFT embedding or QM/MM methods can be used to extend the applicability of ab initio methods to large systems of chemical or biochemical interest.