Autophagy is an evolutionarily conserved process that plays a key role in the maintenance of overall cellular health. While it has been suggested that autophagy may elicit cardioprotective and pro-survival modulating functions, excessive activation of autophagy can also be detrimental. In this regard, the zebrafish is considered a hallmark model for vertebrate regeneration, since contrary to adult mammals, it is able to faithfully regenerate cardiac tissue. Interestingly, the role that autophagy may play in zebrafish heart regeneration has not been studied yet. In the present work, we hypothesize that, in the context of a well-established injury model of ventricular apex resection, autophagy plays a critical role during cardiac regeneration and its regulation can directly affect the zebrafish regenerative potential. We studied the autophagy events occurring upon injury using electron microscopy, in vivo tracking of autophagy markers, and protein analysis. Additionally, using pharmacological tools, we investigated how rapamycin, an inducer of autophagy, affects regeneration relevant processes. Our results show that a tightly regulated autophagic response is triggered upon injury and during the early stages of the regeneration process. Furthermore, treatment with rapamycin caused an impairment in the cardiac regeneration outcome. These findings are reminiscent of the pathophysiological description of an injured human heart and hence put forward the zebrafish as a model to study the poorly understood double-sword effect that autophagy has in cardiac homeostasis.Autophagy is an evolutionarily conserved self-degradation process that involves the engulfment, degradation and recycling of dysfunctional or damaged cellular components 1 . It assumes key roles during adaptation to nutrient starvation 1,2 elimination of pathogens 3 , while it is fundamental in cell differentiation and tissue patterning during development 4 and regeneration 5-7 . In the heart, autophagy has been found to be essential for cardiac development, morphogenesis and cardiomyocyte differentiation 8-10 , and is recognized as a highly relevant housekeeping mechanism for the maintenance of the post-mitotic, essentially unreplaceable, cardiomyocytes that constitute it 11 . On the other hand, autophagy has been found to be involved in the onset and progression of many cardiovascular diseases, such as myocardial infarction and chronic heart failure, where it is a riddle how autophagy may have a protective role, while at the same time, aggravating cardiac dysfunction 12,13 . Because of this, autophagy has been recognized as a potential therapeutic target for cardiovascular diseases, though finding the right strategy to use autophagy activation to improve clinical outcome has not been possible until now 14,15 .The zebrafish (Danio rerio) has become a popular vertebrate model organism because of its superb regenerative capacities. Experimental models of heart amputation 16 , cardiomyocyte-specific genetic ablation 17 , hypoxic damage and ischemia/reperfusion ...