This article concerns the problem of Indonesia's counterterrorism measures after the 9/11 terrorist attack; its difficulties, achievements and prospects. This article is relevant owing to the fact that after the defeat of ISIS in the Middle East Southeast Asia risks becoming the main center of terrorist activity. Indonesia as a country with the largest Muslim population (229 million, far more than in, for instance, Saudi Arabia, the keeper of two shrines, with merely 31,8 million Muslims) is likely to be most affected by this fact. This article consists of two parts. In the first part the main problems, which Indonesia faces, are considered. Among them are the predominance of Muslims whose opinion on this matter cannot be ignored, ineffective cooperation between the ASEAN countries, the support of radical Islam among the most educated citizens, the issue of the increase of the army's role in the state and their involvement in terrorist activity, the issue of repatriation of terrorists of Indonesian origin and members of their families from other countries, facelessness of the political parties and vacuum in some areas of political spectrum, especially left, which leads to lack of real choice. The second part is devoted Indonesia's international cooperation in terms of counterterrorist activity. Cooperation with the US and Russia is quite possible. There is need to aid the Philippines and Myanmar, which are torn by internal conflicts, which attract radicals from many countries. Indonesia's most promising allies are its neighbours: Thailand, Malaysia and Singapore, which are quite effective in tackling the issue of terrorism. During the last few years the cooperation between the ASEAN countries has been quite flourishing, and the sides are moving from negotiations to real actions, such as sharing information and experience, patrolling borders together. The main point, which will determine the success of ASEAN cooperation is willingness to interfere in internal matters of the members when it is necessary.