Some of the most serious threats to network security involve malware. One common way to detect malware-infected machines in a network is by monitoring communications based on blacklists. However, such detection is problematic because (1) no blacklist is completely reliable, and (2) blacklists do not provide the sufficient evidence to allow administrators to determine the validity and accuracy of the detection results. In this paper, we propose a malicious DNS query clustering approach for blacklist-based detection. Unlike conventional classification, our cause-based classification can efficiently analyze malware communications, allowing infected machines in the network to be addressed swiftly.