BACKGROUND: We compared the BACTEC Peds Plus (Becton Dickinson, USA) and BacT/Alert PF (bioMerieux, France) pediatric blood culture bottles in the context of recovery and time to detection (TTD) of bacteria and fungi from pediatric patients. METHODS: Blood samples were collected for culture from pediatric patients who were hospitalized during 2010 at a university hospital. BACTEC Peds Plus and BacT/Alert PF bottles were placed in the BACTEC FX and BacT/Alert 3D blood culture system, respectively, and tested for 5 days. Bottles flagged by instruments as positive were removed from the instruments and the TTDs were recorded. RESULTS: A total of 5,018 sets (1 set, 1 BACTEC Peds Plus and 1 BacT/Alert PF) were evaluated. Overall, the recovery proportions for BACTEC Peds Plus and BacT/Alert PF bottles were 57% (134/195) and 69% (112/195), respectively. There was a significant difference between the 0.38% contamination rate in BacT/Alert PF bottles and the 0.16% contamination rate in BACTEC Peds Plus bottles (P=0.035). The average TTD for all microorganisms was significantly decreased for the BACTEC Peds Plus bottles (P=0.021), but was increased for Candida parapsilosis compared to the results for the BacT/Alert PF bottles (P=0.028). CONCLUSION: We conclude that the rate of detection and contamination is higher when BacT/Alert PF bottles are used than when BACTEC Peds Plus bottles are used for pediatric blood culture. The BACTEC Peds Plus bottles detect nearly all enrolled microorganisms significantly faster than do the BacT/Alert PF bottles.