Adenosine receptors (ARs) are signaling molecules ubiquitously expressed in a wide variety of tissues in the human body. ARs mediate physiological functions by interacting with four subtypes of G-protein-coupled receptors, namely A1, A2A, A2B and A3. The A3 AR, probably the most studied subtype, is also ubiquitously expressed, with high levels in peripheral organs and low levels in the brain. This type of AR is involved in a variety of important patho-physiological processes, ranging from modulation of cerebral and cardiac ischemic damage to regulation of immunosuppression and inflammation. Consequently, the development of potent and selective A3 AR ligands as promising therapeutic options for a variety of diseases has been a prime subject of medicinal chemistry research for more than two decades. Among the plethora of approaches applied quantitative structure activity relationships (QSAR) stands out for being largely employed due to their potential to increase the efficiency at initial stages of the drug discovery process. So, we provide a review of the main QSAR studies devoted to the design, discovery and development of agonist and antagonist A3 adenosine receptor ligands. Common pitfalls of these QSAR applications and the current trends in this area are also analyzed.