The storage of molecular ions in a quadrupole ion trap in combination with reflectron time-of-flight mass spectrometry, jet cooling and multiphoton laser ionization is presented. Jet-cooled molecules are introduced as neutrals into the ion trap and ionized by multiphoton absorption. Varying the storage time causes a dramatic change in the ion intensities, depending on their m/ z ratio. This observation cannot be explained by electronic synchronization effects, but is identified as secular motions of the stored ions. In this paper it is demonstrated that for a time span of up to several milliseconds the ions remain coherent in space and kinetic energy. The molecular ions as well as their fragment ions are not dispersed in the ion trap but move in close ion clouds describing Lissajous trajectories. Consequently, the distance between the middle of the ion trap and the ion cloud periodically changes, resulting in a storage time dependence on mass resolution, flight time and signal intensity. The influences of storage time and other trapping parameters as well as their effect on the interpretation of the results, which are obtained in investigations of time-resolved ion processes, will be discussed.