This study is based on the idea that emotion-related processing happens on various different levels. Common methods that are used to measure different aspects of emotion-related processing exhibit specific sensitivities to one or the other of these separate processing levels. Here, the hypothesis was tested that explicit and implicit measures of emotion-related processing are differently influenced by self-referenced versus unreferenced emotion. The explicit measure was self reported valence and the implicit measure was startle reflex modulation. In one session, emotional scenes were paired with short sentences inducing self-reference (e.g. “this dog will attack you” written underneath the image of an aggressive dog), while in another session, emotional scenes were presented without any reference. During both sessions explicit as well as implicit responses were collected. Self-referenced unpleasant images were rated more negative and self-referenced pleasant images were rated more positive than images with no reference. In contrast, the implicit measure indicated greater startle responses related to self-reference regardless of emotion category. Under the common assumption that greater startle responses reflect increased affective negativity, this means that self-referenced pleasant images elicited more negative implicit affect than unreferenced pleasant images. However, in both cases (self-referenced and unreferenced) startle responses demonstrated valence depended modulation as expected. Thus, in our study startle responses demonstrated sensitivity to affective valence as well as self-reference. It is concluded that self-reference is linked to increased motivation, which in turn has been reported to be detectable via startle reflex modulation (SRM) as well.