microRNAs (miRNAs) are small non-coding RNAs with important post-transcriptional regulatory functions. miRNA-21 (miR-21) is upregulated and miR-143 and miR-145 are downregulated in colorectal carcinoma. The aim of our study was to determine if these miRNAs change their expression levels in response to neoadjuvant chemoradiotherapy in advanced rectal cancer. Forty patients with advanced rectal cancer (clinical uT3/T4 Nx) were included. All patients underwent neoadjuvant chemoradiotherapy and surgical resection. Expression of miR-21, -143 and -145 was examined in macrodissected tumor tissue before and after chemoradiotherapy and normal rectal tissue from the resection specimen. RNA was extracted from formalin-fixed and paraffin-embedded tissue by TRIzol method, polyadenylated, reverse transcribed and analyzed by real-time PCR. Therapy response was assessed according to pathological tumor regression. miR-21 was more highly expressed in tumor tissue than in non-tumorous tissue. However, there was a moderately lower expression in post-therapeutic tumor tissue compared to pre-therapeutic tumor tissue. There was a significant upregulation of miR-143 and miR-145 in post-therapeutic tumor tissue compared to pre-therapeutic tumor tissue. According to the predictive and prognostic value of the analyzed miRNAs, a significant correlation between miR-145 expression and tumor regression was seen. Patients with a low intratumoral post-therapeutic expression had significantly more often a worse response to neoadjuvant therapy compared to patients with a high expression of miR145. The present results support the hypothesis that chemoradiotherapy can profoundly alter miRNA expression profiles. miRNAs might play important roles as molecular biomarkers in the prediction of response to treatment and prognosis.