To distinguish between febrile infants with cerebrospinal fluid pleocytosis who are finally diagnosed with Kawasaki disease and those with enterovirus meningitis poses a diagnostic challenge. We compared clinical and laboratory features at admission between two groups of infants, aged 30-90 days, to identify markers of Kawasaki disease that initially presented as cerebrospinal fluid pleocytosis. During a 2-year period, 100 patients exhibiting cerebrospinal fluid pleocytosis were studied, including six (6.0%) with Kawasaki disease and 30 (30.0%) with enterovirus meningitis. A longer duration of fever before admission (P < 0.01), higher absolute neutrophil count (P < 0.01), increased C-reactive protein level (P < 0.01), pyuria (P = 0.02), and less prominent cerebrospinal fluid pleocytosis (P = 0.01) were identified as initial features of infants finally diagnosed with Kawasaki disease. No significant differences were evident in white blood cell count; platelet count; levels of hemoglobin, alanine aminotransaminase, aspartate aminotransferase, albumin, and sodium; cerebrospinal fluid chemistry; or presence of a rash. Our observations may offer early indicators of Kawasaki disease for timely diagnoses in febrile infants with cerebrospinal fluid pleocytosis.