The aim of the present study was to investigate the utility of 3D cell culture and in vitro cytotoxicity assays, performed using cells derived from biopsies obtained prior to the initiation of preoperative chemoradiotherapy (preop-CRT), in predicting tumor response to chemoradiotherapy following preop-CRT in rectal cancer. Biopsies were obtained from 49 patients with locally advanced rectal cancer that underwent preop-CRT between August 2015 and March 2017. Tumor tissue was obtained before initiating preop-CRT. The response to chemoradiation was assessed by in vitro cytotoxicity assay following 3D cell culture and radiation treatment. The associations between the results from the cytotoxicity assay, and tumor regression grade (TRG) and yp node (ypN) positivity were investigated. Among 49 patients, 26 patients were available for analysis. Cytotoxicity ranged from 25.5-72.6% (median, 47.6%). There was no difference in cytotoxicity according to the TRGs 1-5 (P=0.940), or good tumor response (TRGs 1-2 vs. TRGs 3-5; P=0.729). However, there was a significant difference in cytotoxicity between the ypN-negative and -positive groups (53.2±14.1 and 38.7±10.1, respectively; P=0.021). Following dichotomization of patients with 45% cut-off value, the cytotoxicity assay was the only factor that predicted ypN positivity in multivariate analysis (odds ratio, 13; 95% confidence interval, 1.2-133.2; P= 0.031). In conclusion, the cytotoxicity assay using the 3D cell culture method can be used to predict tumor response, particularly ypN positivity, in patients with rectal cancer who are scheduled for preop-CRT.