We applied a novel approach to respiratory waveform analysis--Monotone Signal Segments Analysis (MSSA) on 6-h recordings of respiratory signals in rats. To validate MSSA as a respiratory signal analysis tool we tested it by detecting: breaths and breath-to-breath intervals; respiratory timing and volume modes; and changes in respiratory pattern caused by lesions of monoaminergic systems in rats. MSSA differentiated three respiratory timing (tachypneic, eupneic, bradypneic-apneic), and three volume (artifacts, normovolemic, hypervolemic-sighs) modes. Lesion-induced respiratory pattern modulation was visible as shifts in the distributions of monotone signal segment amplitudes, and of breath-to-breath intervals. Specifically, noradrenergic lesion induced an increase in mean volume (p<or=0.03), with no change of the mean breath-to-breath interval duration (p>or=0.06). MSSA of timing modes detected noradrenergic lesion-induced interdependent changes in the balance of eupneic (decrease; p<or=0.02), and tachypneic (an increase; p<or=0.02) breath intervals with respect to control. In terms of breath durations within each timing mode, there was a tendency toward prolongation of the eupneic (p<or=0.08) and bradypneic-apneic (p<or=0.06) intervals. These results demonstrate that MSSA is sensitive to subtle shifts in respiratory rhythmogenesis not detectable by simple respiratory pattern descriptive statistics. MSSA represents a potentially valuable new tool for investigations of respiratory pattern control.