The advantages of transdiagnostic protocols for emotional disorders (ED) (anxiety and depression) include the ability to treat multiple psychological disorders using the same treatment protocol, and the capacity to better address comorbidity. Comorbidity in ED has been associated with higher rates of severity, functional impairment, and chronicity. However, no attempts have been made in the literature to systematically review whether these studies include assessments to evaluate the treatment response in comorbid diagnoses, in addition to the principal diagnosis. Moreover, transdiagnostic treatments have been developed for a range of ED, but to date no study has analyzed the real distribution of diagnoses in these studies. The current study aimed to analyze: a) whether treatment response in comorbidity is evaluated in transdiagnostic treatments for ED; b) what diagnoses are targeted in transdiagnostic treatments for ED; and c) the real distribution of the diagnoses at baseline in these studies. A systematic search of the literature was conducted in PsycINFO, PubMed, EMBASE, and the Cochrane Library. Fifty-two randomized controlled trials were identified, with a total of 7007 adult participants. The results showed that, although most of the studies reported data on comorbidity at baseline, only 40% of them examined the effects of the intervention on the comorbid disorders. The most commonly targeted diagnoses in transdiagnostic protocols were panic/agoraphobia, generalized anxiety, social anxiety, and depression. Other disorders, such as obsessive-compulsive disorder, posttraumatic stress disorder, and anxiety/depression not otherwise specified, were marginally included in these studies. Regarding the distribution of diagnoses at baseline, generalized anxiety, panic/agoraphobia, social anxiety, and depression were the most frequently observed, whereas depression not otherwise specified was the least represented. The results highlight the importance of assessing comorbidity in addition to the principal diagnoses in transdiagnostic treatments, in order to draw conclusions about the true potential of these interventions to improve comorbid symptoms. Implications of the current study and directions for future research are discussed.