Alphaviruses, such as Chikungunya and Mayaro, are emerging arthropod-borne pathogens that particularly affect developing countries. Alphavirus infection has great clinical relevance and must be identified and treated properly, as the disease caused by these viruses has a characteristic chronic phase with joint pain that can last for several months or even years, significantly impacting the quality of life of the infected subjects. Animal models of arthritis caused by Alphaviruses allow the study of inflammatory response, bone loss, and tissue damage, providing biological information similar to that obtained in humans. In this chapter, we detail protocols for the process of viral propagation and infection in a murine model, as well as monitoring of the clinical score, plantar edema, and hyper-nociception by methods such as Von Frey filaments and hot plate, in an attempt to better understand the clinical manifestations that occur in humans. This chapter also brings other techniques associated with the study of the disease such as viral titration, micro-CT processing to evaluate bone health parameters, as well as the extraction of neurological tissues associated with the disease and evaluation of antiviral antibodies by ELISA.