Background and Objective: Meningitis is a medical emergency requiring immediate diagnosis and treatment. Bacterial and viral causative agents play a role in meningitis appearance to various degrees. Thus, effective vaccines and antimicrobial and supportive treatments need to be developed and monitoring should be performed in different regions for controlling this disease. Most previous studies have focused on a small number of bacterial agents, and the viral profile of this disease is not precisely monitored in Iran, especially in overpopulated regions. Moreover, limited new applied methods with high precision and sensitivity for the detection of meningitis agents indicate the necessity of determining meningitis agents by rapid molecular methods, which was the aim of the current study.    
Materials and Methods: Overall, 148 samples obtained from suspected meningitis patients from different age groups admitted to Tehran and Karaj hospitals were evaluated by new methods involving specific primers for 16s rRNA, PCR, and Real-time PCR tests. 
Results:  It was found that viral infection, especially infection with human enterovirus, remains the main cause of meningitis in Iran, and Neisseria meningitides is the most common bacterial isolate detected in meningitis cases.
Conclusion: Despite the decreasing trend in meningitis incidence, according to World Health Organization recommendation, implementing an enhanced surveillance system to provide high-quality data on the epidemiological profile of meningitis per each region is necessary.