In clinical routine there is a growing need to encode medical concepts with available standard coding systems. The coding process can be time consuming and may significantly add to daily paperwork, particularly regarding patients with multiple diagnoses and in busy clinical environments with a high turnover of patients. We have developed a generic computerised encoding tool--the PADS encoder--to ensure rapid, correct and complete coding of diagnoses in daily routine. The tool is integrated into an electronic patient record system (PADS, Patient Archiving & Documentation System) and takes full advantage of the user friendly Macintosh interface. The tool was tested in a controlled experiment by 18 clinicians who encoded a total of 666 medical concepts in each protocol (study protocol vs. control). The following positive findings were significantly associated with the use of the computerised coding tool: the number of correctly encoded medical concepts was higher (99.55% vs. 86.1%), coding errors were lower (0% vs. 10.81%), more modifier codes were encoded correctly (increase by up to 43%), less coding errors were made (decrease by up to 43%), the overall rate of correctly encoded and complete main and modifier codes was increased by 31.27% (97.29% vs. 66.02%), coding time was reduced by 50%. This paper presents data to suggest that a computerised coding tool can produce more complete data of higher quality and can save time compared with the traditional approach to encode medical concepts.