1. The objective of this work was to determine whether configurations of midline brain stem neural assemblies change during the respiratory cycle. 2. Spike trains of several single neurons were recorded simultaneously in anesthetized, paralyzed, bilaterally vagotomized, artificially ventilated cats. Data were analyzed with cross-correlational and gravity methods. 3. Sequential samples from each of eight groups of neurons known to contain synchronously discharging neurons exhibited temporal variations in that synchrony. 4. Gravity analysis of short (less than 200-s) samples of spike train data revealed 20 pairs of clustered particles that were not predicted from cross-correlation analysis of the parent data sets (greater than 20 min). 5. Twenty-nine groups of three to eight simultaneously monitored neurons, each with at least two synchronously discharging neurons, were analyzed for evidence of respiratory phase-dependent modulation of that coordinated activity. Spikes from successive interleaved inspiratory and expiratory intervals were analyzed separately. 6. Neurons pairs in 11 groups were more synchronous during the inspiratory interval; six groups had pairs that were more synchronous during the expiratory period. In two groups, different pairs were synchronous in different respiratory phases. In 11 of the 26 pairs that exhibited phase-dependent differences in synchrony, neither neuron had a respiratory-modulated firing rate as judged by either the cycle-triggered histogram or an analysis of variance of their firing rates. 7. Configurations of respiratory-related brain stem neural networks changed with time and the phases of breathing. Neurons with no apparent respiratory modulation of their individual firing rates collectively exhibited respiratory phase-dependent modulation of their impulse synchrony.(ABSTRACT TRUNCATED AT 250 WORDS)