We have investigated the potential of metal-organic frameworks for immobilising single atoms of transition metals using a model system of Pd supported on NH2-MIL-101(Cr). Our transmission electron microscopy and in situ Raman spectroscopy results give evidence for the first time that functionalised metal-organic frameworks may support, isolate and stabilise single atoms of palladium. Using thermal desorption spectroscopy we were able to evaluate the proportion of single Pd atoms. Furthermore, in a combined theoretical-experimental approach, we show that the H-H bonds in a H2 molecule elongate by over 15% through the formation of a complex with single atoms of Pd. Such deformation would affect any hydrogenation reaction and thus the single atoms supported on metal-organic frameworks may become promising single atom catalysts in future.