This study compares and describes factors that differentiate between DENV and CHIKV infections on presentation and describes predictors of persistent arthralgia in CHIKV patients. Patients aged >14 years with acute CHIKV and DENV infections confirmed by the diagnostic virology laboratory from April 2008 to July 2009 were retrospectively identified. Clinical and laboratory data were obtained from medical records and compared. CHIKV patients were older and more likely to be female. CHIKV was independently associated with arthralgia and rash, while DENV was associated with myalgia, raised aspartate transaminase, and leucopenia. Persistent arthralgia was a frequent sequel of CHIKV infection in this cohort.