The aim of the present study was to determine whether used orthodontic wires made of different materials cause toxicity and loss of viability on three-dimensional (3D) cell cultures. Three types of orthodontic wires, stainless steel, Nitinol, and TMA (n = 9) which had been used clinically in fixed appliances for a period of 1 month, were retrieved at random from five patients. Both upper and lower archwires were collected and subjected to two different protocols: to assess toxicity, two pieces of each wire were placed on 3D cell cultures (reconstituted human epithelium); to investigate the possibility of cell damage, the 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl tetrazolium bromide (MTT) assay was used and haematoxylin and eosin staining was performed to evaluate morphological changes. Copper wire served as the control to determine the morphology of severe toxicity, and native cell cultures and silk were used as the negative controls. Morphological evaluation of the native cell cultures revealed no toxic reactions. The ranking, from mild to severe toxicity was as follows: stainless steel < Nitinol = TMA. There were no significant differences between TMA and Nitinol. The MTT assay revealed the following mean percentage values for viability: native cell line (negative control), 100; stainless steel, 102.25; TMA, 87.4; Nitinol, 85.3; and copper wire (positive control) 57.2. Histological evaluation of the 3D cell cultures showed no severe toxicity or loss of viability for any of the wires. However, relative comparison between the different wires revealed that stainless steel induced less toxicity/loss of viability compared with TMA and Nitinol wire.