Base Excision Repair (BER), a predominant pathway to repair small base damages, includes two sub-pathways: a short-patch and a long-patch BER. Since it has been suggested that long-patch BER is dependent on PCNA, it is possible that this pathway is more effective in S phase than in other phases. In this study, to compare the mode of BER in G1 and S phase cells, we first detected the number of MMS-induced AP sites in G1 and S phase cells. We synchronized HeLa RC355 cells in M phase by nocodazole. After releasing the synchronized cells, we examined the number of apparent MMS-induced AP sites in G1 and S phase cells using the ARP method. We found no significant difference between the number of AP sites in both phases, though slightly more AP sites were observed in G1. When compared the total number of methylated bases, we found the number in G1 phase was twice as much as that in S phase cells at 20mM MMS (p<0.05). We have directly analyzed intracellular AP sites using the FARP-1 method. We obtained the similar results as described above. These results suggest that the FARP-1 method is useful to monitor the intracellular BER process. Further analysis is in progress.