Objective The current study was designed to compare the sensitivities of Calcein-AM and Annexin V-FITC for early detection of apoptosis in living cells by flow cytometry and to establish a new method for early detection of apoptosis. Methods The Molt-4 cell line treated with camptothecin (CPT) or ultraviolet(UV) were labeled with Calcein-AM and FITC-conjugated Annexin V respectively, then the apoptosis rate were analyzed by flow cytometry and the performance of Calcein-AM and Annexin V for early detection of apoptosis were compared. Results Our results showed that both probes allowed the detection of apoptotic cells. However, Calcein-AM was more sensitive than Annexin V. We could detect the apoptosis induced by CPT in two hours after inducing with Calcein-AM and in three hours after inducing with Annexin V. The apoptosis induced by UV could be detected in one hours after inducing with Calcein-AM but two hours after inducing with Annexin V. Conclusion Annexin V is less sensitive than Calcein-AM for detection of early apoptosis, and the new method for detection of early apoptosis with Calcein-Am is stable, reliable, sensitive and low-cost.