Beneficial effects of acute bouts of aerobic activity on cognitive functioning have frequently been reported. Most evidence is related to elderly adults, but little is known about this beneficial effect on young adults. Positive effects on cognitive functioning have been reported for a couple of functions. One prominent domain is related to working memory, however little is known about the specific neurophysiological and haemodynamic correlates of the benefit of aerobic exercise on cognitive performance. Only a handful of experiments have used neuroimaging techniques to shed light on the neuronal correlates of aerobic exercise. Here, the neuronal and haemodynamic correlates of the beneficial effects of physical exercise have been investigated and possible methodological problems associated with this approach were evaluated. In our first study we investigated the appropriateness of using fMRI to measure the haemodynamic correlates of cognitive improvement after acute bouts of sub-maximal exercise. Our second study addressed the influence of acute bouts of aerobic activity on two different working memory tasks in relation to reaction time and neuronal patterns of activation measured with fMRI. Finally, the third study was carried out to determine the influence of current fitness level on structural changes in certain brain regions using two different approaches: 1) cortical thickness and 2) structural connectivity based on diffusion-weighted MR data. The first study provides evidence that fMRI is appropriate for use after acute bouts of exercise. Results from the second study suggest that bouts of aerobic activity have selective beneficial effects on cognitive functions in the domain of working memory. These effects were specifically related to highest working memory load. Moreover, the actual level of fitness is associated with specific changes in brain structure.