Recent findings in cognitive neuroscience indicate that activation of anterior cingulate cortex (ACC) is related to detecting cognitive conflict. Conflict related ACC activation elicits responses in central autonomic network which can be assessed by psychophysiological measures such as heart rate variability (i.e. beat to beat R-R intervals - RRI). Recent findings in neuroscience also suggest that cognitive conflict is related to specific nonlinear chaotic changes of the signal generated by the neural systems. The present study used Stroop word-colour test as an experimental approach to the study of cognitive conflict in connection with RRI measurement, psychometric measurement of dissociation (DES) and calculation of largest Lyapunov exponents in nonlinear data analysis of RRI time series in 40 patients with unipolar depression and 35 healthy controls. Significant correlation 0.58 (p < 0.01) between largest Lyapunov exponents and DES found in depressive patients indicate that cognitive conflict related neural interference during conflicting Stroop task is closely related to dissociative processes. These results present first supportive evidence that degree of chaos could be related to dissociation.