Pathogens responsible for meningitis, encephalitis and Neurological related disorders are of clinical significance. Herpes Simplex Virus type 1 and type 2 and Mycobacterium tuberculosis complex are few examples. The current study involved genotyping of Herpes Simplex Virus type 1 and type 2 and characterization of Mycobacterium tuberculosis complex in CSF by molecular methods. 32 CSF specimens from patients with clinical suspicion of viral meningitis and 58 from patients suspected for bacterial meningitis was considered for the molecular characterization of Mycobacterium tuberculosis complex. Among 32 patients, suspected for viral meningitis, 03 cases were HSV type 1 positive, where as 5 cases were with both HSV type 1&2. Among the 58, strongly suspected for Tuberculosis meningitis, 20 (34.4%) were TB PCR positive with 12 (60 %) Male and 8 (40 %) female and 38 cases(65.5 %) were negative. It was seen Adenosine Deaminase was elevated in 30 cases but 28 cases was having less than 10 IU/L. Correct, novel, significant molecular diagnostic tools are very important for all those laboratories performing routine diagnosis of tuberculosis in PCR based laboratories settings.