Diagnosis-related groups (DRGs) are secondary patient classification systems based on primary classified medical data, in which single events of care are grouped into larger, economically and medically consistent groups. The main primary classified medical data are diagnoses and surgery codes. In Sweden, the number of secondary diagnoses per case increased during the 1990s. In the early 1990s some county councils introduced DRG systems. The present study investigated whether the introduction of such systems had influenced the number of secondary diagnoses. The nation-wide Hospital Discharge Register from 1988 to 2000 was used for the analyses. All regional hospitals were included, giving a database of 5,355,000 discharges. The hospitals were divided into those that had introduced prospective payment systems during the study period and those that had not. Among all regional hospitals, there was an increase in the number of coded secondary diagnoses, but also in the number of secondary diagnoses per case. Hospitals with prospective payment systems had a larger increase, starting after the system was introduced. Regional hospitals without prospect payment systems had a more constant increase, starting later and coinciding with the introduction of their DRG-based management systems. It is concluded that introduction of DRG-based systems, irrespective of use, focuses on recording diagnoses and therefore increases the number of diagnoses. Other reasons may also have contributed to the increase. It was found that the changes in the speciality mix, during the study period, have impact on the increase of secondary diagnoses.