OBJECTIVES To determine the etiological agents by Latex Particle Agglutination (LPA) and Polymerase Chain Reaction (PCR) in patients admitted with Cerebrospinal Fluid (CSF) culture negative bacterial meningitis Methods: This descriptive case series was conducted at National Institute of Child Health, Karachi from January 2010 to December 2012. Patients meeting the WHO case definition of suspected meningitis from one month to 59 months of age were included in the study. CSF examination and culture was carried out on every patient and CSF culture negative patients were enrolled. Demographic data, clinical signs & symptoms and laboratory findings were entered into the proforma. Data was analyzed using statistical package for social sciences (SPSS) version 17. P-value <0.05 was taken as significant. RESULTS A total of 166 patients were included. Male were 96 and female were 76 with the male to female ratio of 1.26. The mean age of patient was ± SD 14.6 ± 14.5 months. The etiological agents identified by LPA were in 26/166 (15.66%) cases and the organisms were H. influenzae type b 10 cases, streptococcus pneumoniae 15 cases and meningococcus only one case respectively. The organisms identified by PCR were in 65/166 (39.15%) cases and the isolates were H. influenzae type b 16 cases, streptococcus pneumoniae 48 cases and meningococcus 01 case respectively. CONCLUSION LPA and PCR are superior and useful diagnostic tools in microbiology. They can be used for rapid etiological diagnosis of bacterial meningitis for the early administration of proper antibiotic. Abbreviation: LPA = Latex Particle Agglutination, PCR = Polymerase Chain Reaction, CSF = Cerebrospinal Fluid, CNS = Central Nervous System.