BackgroundThe costing method used can change the results of economic evaluations. Choosing the appropriate method to assess the cost of organ recovery is an issue of considerable interest to health economists, hospitals, financial managers and policy makers in most developed countries.ObjectivesThe main objective of this study was to compare a mixed method, combining top-down microcosting and bottom-up microcosting versus full top-down microcosting to assess the cost of organ recovery in a French hospital group. The secondary objective was to describe the cost of kidney, liver and pancreas recovery from French databases using the mixed method.MethodsThe resources consumed for each donor were identified and valued using the proposed mixed method and compared to the full top-down microcosting approach. Data on kidney, liver and pancreas recovery were collected from a medico-administrative French database for the years 2010 and 2011. Related cost data were recovered from the hospital cost accounting system database for 2010 and 2011. Statistical significance was evaluated at P < 0.05.ResultsAll the median costs for organ recovery differ significantly between the two costing methods (non-parametric test method; P < 0.01). Using the mixed method, the median cost for recovering kidneys was found to be €5155, liver recovery was €2528 and pancreas recovery was €1911. Using the full top-down microcosting method, median costs were found to be 21–36% lower than with the mixed method.ConclusionThe mixed method proposed appears to be a trade-off between feasibility and accuracy for the identification and valuation of cost components when calculating the cost of organ recovery in comparison to the full top-down microcosting approach.Electronic supplementary materialThe online version of this article (doi:10.1186/s13561-016-0133-3) contains supplementary material, which is available to authorized users.