Xiao Chen explains how the HDFS Disk Checker works for data nodes:
The function of block scanner is to scan block data to detect possible corruptions. Since data corruption may happen at any time on any block on any DataNode, it is important to identify those errors in a timely manner. This way, the NameNode can remove the corrupted blocks and re-replicate accordingly, to maintain data integrity and reduce client errors. On the other hand, we don’t want to utilize too many resources, so that disk I/O can still serve actual requests.
Therefore, block scanner needs to make sure that suspicious blocks are scanned relatively quickly, and other blocks are scanned every once in awhile, at a relatively lower frequency, without significant I/O usage.
This is a nice article for operations folks who own Hadoop clusters.