White spot lesions are observed in nearly 50% of patients undergoing orthodontic treatment. Long-lasting antibacterial properties of orthodontic cements can reduce this phenomenon. The aim of this research was to compare antimicrobial activity of three commercial glass ionomer cements with three commercial zinc phosphate cements, over time, against streptococcus mutans and candida albicans. Direct contact test (DCT) was used to evaluate the antibacterial and antifungal activity of products after 48 h and 7 days of incubation. The results demonstrated that all the cements presented antibacterial activity but the antibacterial activity of glass ionomer cements was more than that of zinc phosphate cements. Counts of C. albicans after 48 h were lower and statistically different in the GIC group in relation to the control groups. But no differences were observed between GIC and control groups at 7 days. Based on the results of this study, the antimicrobial and mainly antifungal effects of all the cements were so short.