Autotransplantation is a versatile technique for the replacement of a missing tooth and cryopreservation can expand its scope. The aim of this in vitro study is to compare the antimicrobial effect of different transport protocols on procured teeth prior to cryopreservation. Streptococcus oralis biofilms were grown on ten sterile premolars, incubated for 48 h and subjected to the following transport procedures: an untreated (contaminated) control group, a group rinsed with phosphate buffered saline (PBS), a group transported in PBS, a group transported in Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with fetal calf serum (FCS), and a group transported in DMEM supplemented with FCS and antibiotics (AB). The effect of cryopreservation as such, as well as the combination with a transport medium (DMEM + FCS + AB) on the contamination was also tested. The surviving bacteria were harvested, and determined by plate counting. There was no significant reduction in contamination after rinsing the tooth, after transport in PBS or after transport in DMEM with FCS. Significant reductions were observed for transport in DMEM with AB when compared to the control group (p = 0.003). Cryopreservation as such reduced the biofilm significantly (p < 0.001). No cumulative effect could be found when transport in DMEM + FCS + AB was followed by cryopreservation. Within the limitations of this laboratory set-up, DMEM + FCS + AB was the most effective transport medium in S. oralis biofilm elimination. It could not be concluded that rinsing of the tooth gives an additional reduction. Cryopreservation as such decontaminated the teeth more effectively than any tested transport procedure.