Simulations of structure formation in the standard cold dark matter cosmological model quantify the dark matter halos of galaxies. Taking into account dynamical friction between dark matter halos, we investigate the past orbital dynamical evolution of the Magellanic Clouds in the presence of the Galaxy. Our calculations are based on a three-body model of rigid Navarro–Frenk–White profiles for dark matter halos but were verified in a previous publication by comparison to high-resolution N-body simulations of live self-consistent systems. Under the requirement that the LMC and SMC had an encounter within 20 kpc between 1 and 4 Gyr ago in order to allow the development of the Magellanic Stream, using the latest astrometric data, the dynamical evolution of the MW/LMC/SMC system is calculated backwards in time. With the employment of the genetic algorithm and a Markov-Chain Monte-Carlo method, the present state of this system is unlikely, with a probability of <10−9 (6σ complement), because the solutions found do not fit into the error bars for the observed plane-of-sky velocity components of the Magellanic Clouds. This implies that orbital solutions that assume dark matter halos, according to cosmological structure formation theory, to exist around the Magellanic Clouds and the Milky Way are not possible with a confidence of more than 6 sigma.