Limitations of fluorescence-activated cell sorting (FACS) include: 

• Preparing samples requires careful staining of cells with fluorescent antibodies, which can be a time-consuming process
• Sample recovery rates can vary and are typically lower when isolating rare populations
• Although beneficial in high-throughput applications, too fast a rate can be a limiting factor as it can compromise the cell sorting quality and consequently the data analysis
•  The stress induced on cells during this process, may cause apoptosis, affecting the viability of the cells for subsequent assays
• The cost of FACS can be prohibitive because of the high cost of purchasing and maintaining the necessary equipment
• The equipment can only be operated by highly trained personnel