Polymerase chain reaction (PCR) has been widely used for the detection of bacterial pathogens from various clinical samples. PCR is rewarded as a most sensitive diagnostic method; however, there are a lot of factors that may influence the success of the test, including good sample preparation. A good PCR result always depends on good quality and quantity of DNA extracted from the clinical sample. Currently there are a lot of commercially available DNA extraction kits; however the cost is high, especially so for routine diagnostic used in low resource countries. The purpose of the present study was to compare four DNA extraction protocols to determine the best limit of detection of the organism, total time taken for the DNA extraction and the cost. Cerebrospinal fluid (CSF) samples were spiked with the Streptococcus pneumoniae. Then the extraction of DNA was done by boiling method, lysis and centrifugation, chelex method, and using commercially available DNA extraction kit. The targeted DNA was successfully amplified from all the methods applied, at different limit of detection. We conclude that, of these four methods, lysis method is as good as the commercially available DNA extraction kit in term of limit of detection, at a very low cost.