Although a limited number of service cost estimates exist, no study has evaluated how differences in the method used to collect the staff time allocation across treatment services contribute to differences in service cost estimates. Three alternative data collection methods for estimating service-level costs in methadone treatment programs were evaluated: key informants, staff surveys, and staff diaries. We analyzed data from 25 methadone clinics across the United States. Results indicate that for the three primary services offered at methadone clinics-individual counseling, group counseling, and methadone dosing-no statistically significant differences exist in the mean estimates of costs per session across programs. Of the other five services analyzed, we found no statistically significant differences in two of the mean costs per session and a small but statistically significant difference in another service. We found large and statistically significant differences in mean costs for two services, initial patient assessment and initial medical services. Although there is no gold standard available to judge which method is the best to use, we concluded that the key informant method yields more reliable cost estimates compared with the staff methods and is less burdensome to both the treatment programs and to researchers. Our findings suggest that the key informant method is the preferred method for costing substance abuse treatment services.