OBJECTIVES: Each year approximately 900,000 new cases of hematological malignancies are diagnosed globally. Diagnosis is comprised of multiple modalities, including flow cytometry. Current laboratory developed testing (LDT) for flow cytometry is non-standardized and error prone. Insufficient research has been published evaluating the cost and errors in this space. Manual work, including steps such as antibody selection, compensation, and pipetting have been identified as potential sources of error in flow cytometry. The aim of this study is to quantify the time and associated economic impact of manual work in a flow cytometry process for hematological malignancies.  METHODS: An observational study was conducted at a public Canadian acute care clinical laboratory in collaboration with a lean specialist team for the purposes of workflow analysis. The results of this pilot were used to inform this extended costing analysis. Evaluation of the instrument, reagent, and sample preparation was performed. Total opportunities for error in the workflow were identified (defined as steps involving manual efforts) and manual labor time was then used to estimate indirect costs.  RESULTS: A total of 37 steps were involved in instrument set-up, 81 steps for manual reagent and sample preparation, each of these steps containing multiple opportunities for error. At a 550 bed institution performing 591 leukemia and lymphoma tests annually, it was estimated that a total of 365 hours of manual labor by a skilled medical lab technologist incurred indirect costs of $18,250. CONCLUSIONS: Based on this case study, manual work resulted in substantial cost to the laboratory in indirect costs. This suggests that in addition to reducing the potential for error, minimizing unnecessary manual steps in the flow cytometry workflow could also reduce laboratory indirect costs and improve efficiency. Future research is warranted to quantify the frequency of errors in manual steps in LDT for flow cytometry.