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Studies in health economics especially economic evaluations of health care technologies and programmes are getting more and more important. However, in Germany there are no established, validated and commonly used instruments for the costing process. For the economic evaluation of a rehabilitation programme for patients with chronic lung diseases such as asthma and chronic bronchitis we developed methods for identification, measurement and validation of resource use during the inpatient rehabilitation programme and during the outpatient follow-up period. These methods are based on methodological considerations as well as on practical experience from conducting a pilot study. With regard to the inpatient setting all relevant diagnostic and therapeutic resource uses could be measured basing on routine clinical documentation and validated by using the cost accounting of the clinic. For measuring the use of resources during the follow-up period in an outpatient setting no reliable administrative data are accessible. Hence, we compared a standardised retrospective patient questionnaire used in a 20-minute interview (n = 50) and a cost diary for the continuing documentation by the patient over a period of 4 weeks (n = 50). Both tools were useful for measuring all relevant resource uses in sufficient detail, but because of higher participation rates and lower dropouts the structured interview appears to be more suitable. Average total costs per month were 1591 DM (interview), respectively 1867 DM (cost diary). Besides productivity loss, costs for medication and GP visits caused the relatively highest resource uses. Practicable instruments were developed for the costing process as part of an economic evaluation in a German rehabilitation setting for pulmonary diseases. After individual modification, these could also be used for different indications and in other institutional settings.