To determine the burden of bacterial meningitis and characterize its epidemiology, a laboratory-based surveillance was established in five hospitals in Sudan. Hospital personnel were trained in basic surveillance and bacteriology techniques. Positive cerebrospinal fluid (CSF) cultures were confirmed at Sudan National Laboratories and U.S. Naval Medical Research Unit No. 3. Additionally, 126 frozen CSF samples from culture-negative meningitis cases were tested by polymerase chain reaction (PCR). Of 1,830 suspected meningitis cases enrolled, 75% were less than 5 years old and 63% were males. Of these, 149 (8%) were culture-confirmed, including 121 (81%) Neisseria meningitidis; 18 (12%) Streptococcus pneumoniae, and 10 (7%) Haemophilus influenzae. Of 440 turbid specimens, 132 (30%) were culture-positive. Of the 126 samples from culture-negative meningitis cases that were tested, only 18 (14%) were classified as turbid on gross examination, yet 63 (50%) were positive by PCR. This study suggests that PCR may be useful to more accurately define the burden of disease in epidemic setting. Maintaining laboratory-based surveillance allows evidence-based decision-making and helps monitor the impact of new vaccines introduction.