Respiratory tract infections are caused by different types of virus and bacteria and have become a global health issue. The detection and analysis of respiratory tract pathogens is nowadays performed commonly using PCR technology because of its high sensitivity. The aim of this study was to compare the performance of a new instrument, Starlet IVD with Maglead 12gC for extraction of nucleic acid from respiratory tract samples prior to real time PCR analysis. Frozen positive samples and fresh negative samples from patients were analyzed for respiratory viruses and respiratory bacteria. The samples were extracted on both Starlet IVD and Maglead 12gC. Real time PCR analysis was performed after the extraction to compare the performance between both instruments. A total of 44 virus samples were analyzed with Allplex respiratory panel 2 and 61 bacteria samples analyzed with Allplex respiratory panel 4. The result has shown an acceptable agreement of the PCR analysis (> 95%) for both panels between instruments. Starlet IVD has a higher Ct value compared to Maglead 12gC which led to a variation of 7,1% ± 3,6% in Ct value for Respiratory panel 2 and 10,1 % ± 5,3 % for Respiratory panel 4.  In conclusion, Starlet IVD is an automated instrument that will reduce hand-on-time, the risk of errors and improve the work routine for a better quality of results. Regardless the poor Ct-value, the new instrument has been able to detect almost all respiratory pathogens in the samples.