There have been many clinical trials to collect bone debris utilizing special equipment and to apply in the bone graft procedure simultaneously. Collected bone debris (CBD) may be contaminated by bacteria. This may lead to iatrogenic contamination of recipient sites by grafted bone debris. The purpose of this study was to evaluate the effect of strict suction protocol on the levels of bacterial contamination. Total 41 patients (21 male and 20 female patients) with a mean age of 48.97 were selected in this study. They were randomly divided into two groups in this study. One group consisted of a single-suctioning group, while the other was dual-suctioning group. A bone collecting device was used to collect bone specimens during drilling. Samples were obtained and cultures of CBD were performed. Among the 41 samples of cultured bone debris, only 16 samples yielded viable microorganisms. Microorganisms were detected in the 54.5% (12/22) of single-suctioning group, and in 21.1% (4/19) of dual-suctioning group (p=0.03). The majority of microorganisms were Gram positive cocci. It was shown that erythromycin and clindamycin were more effective than penicillin in the antibiotics sensitivity test. It was concluded that the use of strict suction protocol could reduce the bacterial contamination.