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The field of gamma-ray astronomy opened a new window into the non-thermal universe that allows studying the acceleration sites of cosmic rays and the role of cosmic rays on evolutionary processes in galaxies. The detection of almost one hundred Galactic very-high-energy (VHE: 0.1−100TeV) gamma-ray sources in the Milky Way demonstrates that particle acceleration up to tens of TeV energies is a common phenomenon. Furthermore, the detection of VHE gamma rays from other galaxies has confirmed that cosmic rays are not exclusively accelerated in the Milky Way. The rapid development of gamma-ray astronomy in the past two decades has led to a transition from the detection and study of individual sources to source population studies. To answer the question, whether the VHE gamma-ray source population of the Milky Way is unique, observations of galaxies, for which individual sources can be resolved, are required. Such galaxies are the Magellanic Clouds, two satellite galaxies of the Milky Way, which have been surveyed by the H.E.S.S. experiment in the last decade. In this thesis, data from a total of 450 hours of H.E.S.S. observations towards the Large Magellanic Cloud (LMC) and the Small Magellanic Cloud (SMC) are presented. During the analysis of the data sets, special emphasis is put on the evaluation of systematic uncertainties of the experiment in order to assure an unbiased flux estimation of the potential VHE gamma-ray sources of the Magellanic Clouds. A detailed analysis of the survey data revealed the detection of the gamma-ray binary LMCP3, the most powerful gamma-ray binary known so far, that is located in the LMC, and thus, increases the number of known VHE gamma-ray sources in the LMC to four. No other VHE gamma-ray source is detected in the Magellanic Clouds and integral flux upper limits are estimated. These flux upper limits are used to perform a source population study based on known VHE source classes and existing multi-wavelength catalogues. A comparison of the source populations of the Magellanic Clouds and the Milky Way revealed that no other source in the Magellanic Clouds is as bright as the most luminous VHE gamma-ray source in the LMC: the pulsar wind nebula N 157B, and that one-third of the source population of the Magellanic Clouds is less luminous than the other known VHE gamma-ray sources in the LMC. For only a couple of sources luminosity levels of Galactic VHE sources, that are more than one order of magnitude fainter than the detected sources in the LMC, are constrained. Based on the flux upper limits, differences on the TeV source populations in the Magellanic Clouds and the Milky Way as well as the importance of the source environments will be discussed.