Transcranial magnetic stimulation (TMS) is increasingly used in Cognitive Neuroscience to study functional contributions of a stimulated brain region to cognitive and perceptual processing. TMS-related behavioural effects are often interpreted as reflecting selective disruption of processing primarily within the stimulated region itself. This approach is now being extended by studies that combine TMS with concurrent neuroimaging measures, such as functional magnetic resonance imaging (fMRI). We discuss some recent combined TMS-fMRI studies and their implications for TMS investigations of cognition and perception. An emerging theme is that TMS does not affect only the stimulated region, but can also influence remote brain areas interconnected with the stimulation site. Such 'network' effects of TMS can be anatomically specific, but also context-dependent, changing with the current functional state of the targeted network rather than simply reflecting just fixed, context-invariant anatomical connectivity. Perceptual and behavioural effects of TMS may correspondingly involve TMS influences on remote interconnected brain regions, not solely on the stimulated region itself. Thus, TMS can now be used to study the consequences of functional interactions between the stimulated region and other parts of the network. This may lead beyond strictly modular views of brain function, that emphasize functional properties of single brain areas, towards new perspectives on how functional interactions between remote but interconnected brain regions may support perception and cognition.