Treatment of sporadic cardiac myxoma (CM) has always been a challenging task. Currently, surgical excision remains the only option; however, targeted drug discovery schemes are in progress in order to improve treatment strategies and efficacy. The molecular mechanisms behind CM pathogenesis are still not totally unveiled thus drug target identification is still at early steps, trying to compile structured data on the pathophysiology of CM, targets and targeting moieties. Five critical disease pathways involving molecules of seven functional groups have been recently shown by us to be associated with the pathogenesis of CM. In addition, 15 to 20 drug targets and their targeting molecules have also mapped on pathways in an effort to start decoding the molecular profiles based on which early efforts for CM patient stratification into targeted therapeutic regimes. The present review describes the current data and discusses critical issues in the field of targeted and personalized medicine of CM.