Background Interactive Voice Response Systems (IVRS) and other electronic data collection methods have begun to replace conventional paper diaries as a way to capture daily patient reports. However, these methods have not been compared in head and neck (H&N) cancer patients receiving radiation therapy. Methods 15 subjects with H&N cancer were asked to complete daily IVRS calls and daily paper diaries during radiation therapy. We compared response consistency and comparative adherence across the two methods. Results 86.1% (1920/2231) of participants' responses were consistent between IVRS and paper diaries. 79.5% of the expected number of paper diaries were completed, compared to 66.2% of IVRS phone calls. Conclusions In this pilot study of H&N cancer patients undergoing radiation therapy, concordance was high between responses recorded by paper diaries and IVRS. Although adherence appeared to be higher for the paper diaries, it is possible that they may not have been completed at the proper time.