1. DNA Damage: The incorporation of BrdU can cause DNA damage, potentially affecting the cells being studied. 2. Detection Sensitivity: The method requires careful optimization of detection protocols to ensure specificity and sensitivity, as non-specific binding of antibodies can lead to false positives. 3. Cell Viability: Prolonged exposure to BrdU can be toxic to cells, necessitating careful control of the duration and concentration of BrdU administration.