Periodontal and microbiological characteristic among cleft lip and/or palate patients undergoing fixed orthodontic treatment is of interest. Plaque and saliva samples showed high prevalence of Streptococcus mutans (83%), Lactobacillus spp. (67%), and Porphyromonas gingivalis (55%). In vitro analysis showed significantly greater biofilm formation on stainless steel brackets compared to ceramic brackets (p < 0.01), confirmed by SEM imaging. Elevated levels of IL-1β and MMP-8 in gingival crevicular fluid were positively correlated with microbial load (r = 0.72, p < 0.05). Thus, the influence of bracket material on biofilm formation and local inflammatory response is shown.