Electronic pain diaries and palm-top computers have become increasingly important in clinical research and practice. In a randomized crossover trial, 24 patients suffering from chronic cancer and non-cancer pain completed both the electronic and the paper version of a pain diary based on the Minimal Documentation System (MIDOS) for pain and symptom assessment. This includes daily assessment of pain on an 11-point numeric rating scale and weekly documentation of a short quality-of-life questionnaire. Of 52 patients seen during the baseline phase of this study, 28 could be enrolled and only 24 patients completed both diary versions. The other patients were either physically or intellectually unable to use a palm-top computer or unwilling to participate in this study. After a total of four weeks, patient satisfaction was remarkably higher for the electronic palm-top version, even though a high number of patients were lacking experience in the use of computers. Obvious differences were observed between the versions. There were higher numbers of missing values in the electronic data, and patients tended to retrospectively fabricate information in the paper version. No significant difference between the electronic and paper diary could be found assessing the documented pain and symptom intensity. The electronic diary was used more frequently and patients said its use supported a more regular pharmacotherapy. We conclude that the use of electronic pain diaries is a valid and feasible method for documenting patients' pain perception, though some patients may not be able to operate such a diary version. Electronic palm-top pain diaries provide a high degree of patient satisfaction and can ease data collection for clinical research and practice.