Posttraumatic stress disorder (PTSD) and negative affect (e.g., anger, depression, anxiety), are highly co-occurring. It remains unclear whether changes in PTSD symptoms subsequently impact negative affect, or vice versa. This study assessed associations between moment-to-moment PTSD symptoms and negative affect in a sample of smokers with PTSD to determine directionality of this relationship. Participants (N = 125) enrolled in two smoking cessation studies with co-occurring PTSD and cigarette use completed measures of PTSD and negative affect. Ecological momentary assessment (EMA) methodology was used to record symptoms during a one-week baseline period, during which participants smoked ad lib. Cross-lagged path analyses assessed PTSD symptoms and negative affect for directionality of their relationship, controlling for whether an EMA reading was smoking or non-smoking. Path analyses examined the lagged associations between PTSD symptoms and negative affect. Results found PTSD symptom severity at T-1 was significantly related to negative affect levels at time T, but negative affect at time T-1 was not associated with PTSD symptom severity at time T. Results indicated the model retaining the cross-lagged effect of PTSD symptom severity on negative affect provided better fit to the data than other models. Limitations included use of self-report data, brief measures of symptoms, participants already had PTSD and/or MDD, participants were recruited from a specific clinical population, and use of DSM-IV data. Results suggest PTSD symptoms drive day-to-day fluctuations in negative affect, and highlight the importance of evaluating negative affect in the treatment of PTSD.