Although some modern scholars believe that Homer had at least a basic medical education, given that a plethora of medical terms may be found in his poems, in the case of the pestilence that killed the Achaeans (one of the Hellenic peoples believed to have inhabited the Peloponnese) at Troy, his reference was simply informative. No symptoms were mentioned and the only thing known was that mules and dogs were the first to die. While Delphic Apollo was usually on the side of Peloponnesians, during the Trojan War Apollo Smintheus (the Mouse God) sided with the Trojans. Apollo was invoked as Smintheus by his priest Chryses two times and on both occasions a pestilence ensued. In our paper we try to clarify whether this pestilence, as we believe, was caused by a member of the Alphavirus genus, which can inflict a serious epidemic both on human and animal species, especially in equines.