Neurons in layers 2/3 and 5 of rat motor-cortex vary their firing rates and LFP-relative phases during volitional lever-pull tasks. Using a state-space model of spike-time interactions, we analysed the intra- and inter-layer synchrony of these cells in an attempt to understand the behaviour-dependent flow of information in motor cortex. For the whole trial period, at millisecond precision we found strong desynchrony within L5, little synchrony or desynchrony within L2/3, and a peak in inter-layer synchrony at a zero-lag of L5 spike times. Comparing lever-hold and -pull periods we observed that desynchrony was further enhanced in L5 cell pairs that showed concomitant increases in firing rates, and synchrony across layers increased at negative L5 lags, that is, when we subtracted 2, 4, 6 or 8 milliseconds from L5 spike times. These results suggest that the two layers share significant common inputs and that information flows from the shallow to deep layers specifically during arm movement.