For the purpose of identifying the frequency that enterovirus, leptospires, arbovirus cause aseptic meningitis syndrome (AMS) during non-epidemic periods and comparing patients with and without laboratory evidence for an etiologic agent, 112 patients were selected aged between 3 months and 15 years and a clinical suspicion of AMS and were referred to Couto Maia Hospital, the Infectious and Parasitic Disease Reference Center for Salvador, Bahia. In 44.6% (n=50), the etiologic agent for the diagnosis was laboratory-confirmed: enterovirus was identified in 37.7% (n=42) of the cases by the PCR Amplicor diagnostic kit, cerebrospinal fluid or fecal culture isolation; Leptospira sp. in 7.12% (n=8) by the microagglutination test; and arbovirus in non of the cases by inhibition of passive hemagglutination. In 14 of the 22 enteroviral isolates that were evaluated, 6 different serotypes were identified with Echovirus-4 being the major serotype (27.2%; 6/22) among all found (Coxsackie B2, B3, B6 and B9; Enterovirus 71). In conclusion, enteroviruses were the most frequent etiologic agent of AMS and that leptospirosis should be included in the differential diagnosis. In addition, patients with and without laboratory-confirmed identification of the etiologic agent had similar demographic and clinical characteristics and cerebrospinal fluid findings (p >0.05), therefore suggesting that patients without a confirmed diagnosis had enteroviral or leptospiral etiologies.