Most psychophysiological studies of PTSD have not assessed physiological recovery, correlational relationships between PTSD severity and physiological measures within clinical populations, or mediation by cognitive appraisal. Relationships of PTSD severity to psychophysiological reactivity (to acoustic startle), habituation, and recovery were assessed in 29 combat veterans, and mediation by cognitive appraisal (perceived threat and coping ability) was assessed in a subset (n = 16) of participants. Heart rate (HR) recovery was linearly related to PTSD severity. Perceived ability to cope with the lab task, but not perceived threat inherent in the task, mediated the HR recovery—PTSD association. Potential implications of delayed HR recovery for functioning, treatment outcome, and health-risk in PTSD are presented. Cognitive appraisal may represent an important target for treatments.