Visual words that are masked and presented so briefly that they cannot be seen may nevertheless facilitate the subsequent processing of related words, a phenomenon called masked priming. It has been debated whether masked primes can activate cognitive processes without gaining access to consciousness. Here we use a combination of behavioural and brain-imaging techniques to estimate the depth of processing of masked numerical primes. Our results indicate that masked stimuli have a measurable influence on electrical and haemodynamic measures of brain activity. When subjects engage in an overt semantic comparison task with a clearly visible target numeral, measures of covert motor activity indicate that they also unconsciously apply the task instructions to an unseen masked numeral. A stream of perceptual, semantic and motor processes can therefore occur without awareness.