Psychological factors and the autonomic nervous system (ANS) are implicated in the pathogenesis of inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). This study aimed to assess, firstly the way IBS and IBD patients cope with their pathology according to their affective adjustment and secondly the possible links between these affective adjustments and ANS reactivity. Patients with Crohn's disease (CD; n=26), ulcerative colitis (UC; n=22), or IBS (n=27) were recruited and compared to 21 healthy subjects based on psychological variables (trait- and state anxiety, depressive symptomatology, negative mood, perceived stress, coping, health locus of control) and sympatho-vagal balance through heart-rate variability monitored at rest. A principal component analysis, performed on all affective variables, isolated a leading factor labelled as “affective adjustment”. In each disease, patients were distributed into positive and negative affective adjustment. In all the diseases, a positive affect was associated with problem-focused coping, and a negative affect with emotion-focused coping and external health locus of control. Results show that the sympatho-vagal balance varied according to the disease. In CD presenting positive affectivity, an adapted high sympathetic activity was observed. In UC, a parasympathetic blunt was observed in the presence of negative affectivity and an equilibrated sympatho-vagal balance in the presence of positive affectivity. In contrast, in IBS, an important dysautonomia (with high sympathetic and low parasympathetic tone) was constantly observed whatever the affective adjustment. In conclusion, this study suggests that the equilibrium of the ANS is differentially adapted according to the disease. This equilibrium is conjugated with positive affective and cognitive adjustment in IBD (CD and UC) but not in IBS.