When ambiguous visual stimuli are being looked at, perception alternates spontaneously between two competing interpretations of the same sensory input. One major issue in understanding the underlying neural process is whether spontaneous percept switches result from fluctuations at the level of sensory processes or whether they are initiated by higher-order areas. To further study this question, we developed an ambiguous apparent motion paradigm that specifically focused on the generation of percept switches. The percept switches occurred either spontaneously or were experimentally triggered. The differential analysis of spontaneous and triggered percept switches was aimed at disentangling the causes and effects of percept switches. Spontaneous percept switches were associated with stronger activations at the right occipitotemporal junction, whereas prefrontal, superior temporal and inferior parietal regions showed greater activations during experimentally triggered percept switches. We propose that complex networks including both sensory and higher-order areas are involved in percept switches, whereas stimulus-specific sensory processes are crucial for the initiation of spontaneous percept switches.