In the present study we used a proteomic approach to identify and quantify protein abundance differences between male and female zebrafish heart to explore, at the molecular level, any possible sex-biased differences in the heart as the central part of the cardiovascular system for this model organism. The results from the study provide a novel and wide proteome resource, which could be further used to study the role of the identified proteins in the cardiovascular system in both sexes. Furthermore, we hope that this study may open a new window towards the development of sex and gender-based drugs and it establishes sex as a factor to be considered when designing toxicological experiments.