In a prospective comparative study, the use of combined analysis of upper respiratory tract swab samples and cerebrospinal fluid (CSF) samples was assessed to improve the detection rate of enteroviral meningitis in children. An enterovirus was detected in 32% of patients with aseptic meningitis when testing CSF samples alone compared with 71.5% when combining CSF and respiratory tract findings. An enterovirus was detected in 17% of respiratory tract samples in an age- and sex-matched control group without meningitis. Thus, combining the examination of upper respiratory tract with CSF findings may improve the detection rate of enteroviral meningitis. Upper respiratory tract samples should be included in the diagnosis scheme to differentiate benign enteroviral meningitis from other life-threatening infections of the central nervous system.