We aimed to assess clinical and laboratory differences between dengue and chikungunya in children <24 months of age in a comparative study. We collected retrospective clinical and laboratory data confirmed by NS1/IgM for dengue for 19 months (1 January 2013 to 17 August 2014). Prospective data for chikungunya confirmed by real-time polymerase chain reaction were collected for 4 months (22 September 2014-14 December 2014). Sensitivity and specificity [with 95% confidence interval (CI)] were reported for each disease diagnosis. A platelet count <150 000 cells/ml at emergency admission best characterized dengue, with a sensitivity of 67% (95% CI, 53-79) and specificity of 95% (95% CI, 82-99). The algorithm developed with classification and regression tree analysis showed a sensitivity of 93% (95% CI, 68-100) and specificity of 38% (95% CI, 9-76) to diagnose dengue. Our study provides potential differential characteristics between chikungunya and dengue in young children, especially low platelet counts.