Abstract Background In Singapore, the first local outbreak of chikungunya was reported in January 2008, followed by a larger outbreak occurred in August 2008. During the initial outbreak period, a strict containment strategy was adopted and all chikungunya PCR-confirmed cases were isolated and hospitalised at the designated national outbreak management centre. Objectives To detail daily clinical and laboratory features of chikungunya cases during acute illness, and determine factors associated with persistent arthralgia at week 6. Study design Prospective cohort study of patients with PCR-confirmed chikungunya infection and hospitalised within 5 days of illness onset, from 1st August to 10th November 2008. Post-hospital discharge, patients were followed up at the specialist outpatient clinic, and assessed for arthralgia at week 6 of illness. Results Of the 97 patients in the study, the most common presenting symptoms were fever (89.7%) and arthralgia (87.6%). Mean nadir leukocyte and platelet counts were 3.5(SD 1.9) × 10 9/L and 165(SD 42) × 10 9/L respectively. Of the 39 patients who were evaluated at week 6, 14 (35.9%) had persistent arthralgia. Those with persistent arthralgia tended to be females ( p = 0.003), and had a lower peak creatinine level ( p = 0.036) than those without. Peak viral load ( p = 0.664), and duration of fever ( p = 0.056) and viremia ( p = 0.55) respectively, were not significantly different between those with persistent arthralgia and those without. Conclusions This study details the daily clinical and laboratory features of chikungunya patients during acute illness. Those with persistent arthralgia tended to be females, who had significantly lower peak creatinine level.