Introduction: Sterilisation using peracetic acid (PAA) has been advocated for orthodontic elastic bands. However, cane-loaded elastomeric ligatures can also become contaminated during processing, packaging, and manipulation before placement in the oral cavity and are therefore susceptible, and possible causes, of cross-contamination. Aim: To test the hypothesis that 0.25% peracetic acid (PAA), following the sterilisation of elastomers, influences the cytotoxicity of elastomeric ligatures on L929 cell lines. Materials and methods: Four hundred and eighty silver elastomeric ligatures were divided into 4 groups of 120 ligatures to produce, Group TP (latex natural, bulk pack, TP Orthodontics), Group M1 (Polyurethane, bulk pack, Morelli), Group M2 (Polyurethane, cane-loaded, Morelli) and Group U (Polyurethane, cane-loaded, Uniden). Of the 120 ligatures in each group, 100 were sterilised in 0.25% PAA at time intervals (N = 20) of 1 hour, 2 hours, 3 hours, 4 hours and 5 hours. The 20 remaining elastomeric ligatures in each group were not sterilised and served as controls. Cytotoxicity was assessed using L929 cell lines and a dye-uptake method. Analysis of variance (ANOVA), followed by the Tukey post hoc test (p < 0.05) determined statistical relevance. Results: There was a significant difference between TP, Morelli and Uniden elastomerics (p < 0.05), but no difference between the two types of Morelli elastomerics at the 1 hour time interval. In addition, there was a significant difference between Group CC and the other groups assessed, except between Groups CC and TP at the 1 hour time interval. The non-sterilised elastomeric ligatures showed similar cell viability to that observed after 1 hour of standard sterilisation. Conclusion: PAA did not significantly influence the cytotoxicity of elastomeric ligatures after a sterilisation time of 1 hour and is therefore recommended for clinical use.