The aim of this study was to elucidate the interplay between posttraumatic stress disorder (PTSD), substance use disorder (SUD), dissociation and under-regulation of affect in PTSD patients with and without SUD. Research concerning both dissociation and under-regulation in PTSD patients with and without SUD is sparse. Further exploration of these associations may help construct better therapies, especially for patients suffering from both disorders. We studied 103 patients with PTSD, 82 with PTSD+SUD and 58 with SUD and explored the differences in number of trauma, severity of PTSD, (pathological) dissociation and under-regulation of affect. Additionally, we evaluated the moderating role of under-regulation on dissociation and severity of PTSD symptoms in the PTSD and PTSD+SUD group and asked patients about their subjective emotional function of substance abuse. PTSD and PTSD+SUD patients showed significantly more dissociation than SUD patients, but there was no difference between the PTSD and PTSD+SUD group when controlled for age and gender. The PTSD patients did have heightened levels of pathological dissociation and under-regulation compared to both SUD and PTSD+SUD patients. Under-regulation was a predictor of PTSD severity in the PTSD group, whereas dissociation was significant in both the PTSD and PTSD+SUD group. Under-regulation did not moderate the relationship between dissociation and severity of PTSD symptoms in either group. PTSD+SUD patients used substances more often ‘to feel less emotions’ than the SUD group. The discussion reflects on the ‘chemical dissociation hypothesis’ and suggests structural screening for PTSD and dissociation in PTSD+SUD patients as well as integrated treatment.