The objective of this study was to quantify, in vitro and in vivo, bacterial endotoxin (LPS) attached to esthetic elastomeric orthodontic ligatures made of polyurethane and silicone using the Limulus Amebocyte Lysate test (LAL). For the in vitro study, were used four types of aesthetic elastomeric ligatures: Sani-Ties (polyurethane) and Sili-Ties (silicone) -GAC, and Mini Single Case Ligature Stick (polyurethane) and Synergy ® Low-friction ligatures (silicone) -Rock Mountain; 5 of each were contaminated with endotoxin solution (positive control) and 5 non-contaminated (negative control). Replicas made of twisted wire ligatures and of cast stainless steel, of the same size and shape than the elastomeric ligatures, contaminated or not with endotoxin, were used as control. Endotoxin quantification was performed using the LAL test (QCL-1000™ kit), the results being expressed in EU/mL. In the in vivo study, 20 patients of both genders, with ages ranging from 15 to 30 years old, who started treatment with a fixed orthodontic appliance at the School of Dentistry of Ribeirão Preto -University of São Paulo, received randomly the same four types of elastomeric ligatures used in the in vitro study, being a ligature of each brand inserted in the upper and lower canines (UR3, UL3, LR3, LL3), randomly. Twenty-one days later, ligatures were removed and processed for quantification of bacterial endotoxin, using the same test as the in vitro study. All data were submitted to appropriate statistical analysis according to the data distribution, using Kruskal-Wallis tests and Dunn post-test (in vitro study) and ANOVA of repeated measurements and Tukey's post-test (in vivo study). All analyzes were performed using the Graph Pad Prism 4.0 program, with a significance level of 5%. According to the results obtained, it was observed that the bacterial endotoxin attached to all materials tested. In the in vitro study, the GAC silicone group had the lowest median contamination (1.15 EU/mL), in relation to the other groups (p<0.0001), which did not present a statistically significant difference when compared to each other (p>0.05). In the in vivo study, similar to that observed in the in vitro study, the GAC silicone group had the lowest mean contamination (0.577 ± 0.017 EU/mL), with a statistically significant difference (p<0.001) compared to the others groups. It could be concluded that bacterial endotoxin exhibited affinity for the tested silicone and polyurethane aesthetic elastomeric ligatures. The silicone ligatures of GAC brand were the ones that presented less amount of endotoxin attached to their surfaces.