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Objective: The aim of the present study was to analyze two DNA extraction methods for use in molecular GBS diagnostics and compare them to the results of culture method. Materials and methods: Two hundred vaginal samples were collected during the antenatal period, as per CDC recommendations, and atr gene polymerase chain reaction (PCR) was performed. Results: Comparison of the two DNA extraction methods demonstrated 45% concordance. Sensitivity and specificity for 5 M Guanidine DNA extraction were 100% and 86.5%, respectively. Sensitivity and specificity for the commercial DNA extraction kit were 50% and 95%, respectively. Conclusion: This study demonstrated that 5 M Guanidine DNA extraction was superior to the commercial kit, with PCR presenting a shorter turnaround time than culture. PCR could improve sensitivity and, therefore, may be a useful screening method. Sensitive GBS diagnosis allows for an effective treatment, with decreased newborn morbidity and mortality; therefore, cost-effectiveness studies are necessary to assess the feasibility of implementing PCR in routine laboratories, together with maternity ward collaboration.