BackgroundStem cell apheresis in the context of autologous stem cell transplantation requires an accurate cluster of differentiantion 34 (CD34+) count determined by flow cytometry as the current gold standard. Since flow cytometry is a personnel and time‐intensive diagnostic tool, automated stem cell enumeration may provide a promising alternative. Hence, this study aimed to compare automated hematopoietic progenitor enumeration carried out on a Sysmex XN‐20 module compared with conventional flow cytometric measurements.MethodsOne hundred forty‐three blood samples from 41 patients were included in this study. Correlation between the two methods was calculated over all samples, depending on leukocyte count and diagnosis.ResultsOverall, we found a high degree of correlation (r = 0.884). Furthermore, correlation was not impaired by elevated leukocyte counts (>10 000/μL, r = 0.860 vs <10 000/μL, r = 0.849; >20 000/μL, r = 0.843 vs <20 000/μL, r = 0.875). However, correlation was significantly impaired in patients with multiple myeloma (multiple myeloma r = 0.840 vs nonmyeloma r = 0.934).SummaryStem cell measurement carried out on the Sysmex XN‐20 module provides a significant correlation with flow cytometry and might be implemented in clinical practice. In clinical decision‐making, there was discrepancy of under 15% of cases. In multiple myeloma patients, XN‐20 should be used with caution.