The 'correspondence problem' refers to the ambiguity of apparent motion (AM) paths if several similar objects are displaced across successive displays. We investigated the effect of intrinsic object properties such as colour and luminance on AM paths, and used functional magnetic resonance imaging to localize neural correlates of correspondence matching in visual cortical regions. Human subjects looked at an AM display where two dots in diagonally opposite corners of an implicit rectangle were flashed in alternation with two dots in the other two corners, yielding spontaneous alternations between horizontal and vertical AM. The dots differed in colour or luminance, or were identical. Neural activity was analysed as a function of whether the perceived AM path matched the dots' colour or luminance, and was also compared to activity during bistable AM displays without correspondence cues. When AM paths matched colour and luminance cues, activity in early visual cortex was the same as during perception of uncued displays, whereas it was suppressed when perceived AM paths violated colour or luminance cues. Colour-sensitive extrastriate cortex (V4 complex) transiently activated whenever AM perception switched from a pattern violating colour correspondence to one consistent with colour. We propose that the neural correlate of correspondence in early visual cortex reflects regulatory mechanisms that flexibly gate early visual feature processing in accord with an overriding perceptual decision. Conversely, activation of feature-selective extrastriate regions depends on the type of cue used for correspondence matching and may reflect the salience of percepts that match in colour and motion.