We report on three different experiments on high temperature superconducting (HTS) cuprates and colossal magnetoresistive (CMR) manganites, which clearly bring out some of the important similarities and differences between the two material systems. The experiments involve the measurement of temperature dependence of the mean squared displacement of Cu and Mn ions from their equilibrium site in the case of the cuprates and the manganites, respectively, and their correlation with the transport property. In both cases the key ions in the materials (Cu for HTS and Mn for CMR) exhibit vibration amplitudes larger than that of ions in simple Debye solids and clearly show discontinuities in the vibration amplitudes as a function of temperature close to the phase transition temperatures. These point to the unequivocal participation of phonons in the transport processes and possibly in the onset of the phase transitions (i.e. superconductivity and ferromagnetism). The second set of experiments, involves femtosecond optical excitation of micro-strip resistors made of cuprates or manganites, and the subsequent measurement of the changes in the impedance on a 20 ps time scale. In the case of the manganites one measures the time scales involved in the ionization and reformation of a Jahn–Teller polaron and also the decay times of magnon excitors. In the case of the cuprates one sees a highly efficient pair breaking process with a very sharp resonance, with a width of only 100 meV, which is indicative of the role of a large intermediate excitation in the mechanism of high temperature superconductivity. In the third experiment, spin-polarized electrons injected from a manganite electrode into a superconductor are observed to break pairs at a rate far larger than unpolarized electrons. This effect seems very orientation dependent for the case of YBCO, which may shed new light on the transport of quasi-particles at YBCO interfaces.