General speaking, the .gz extension will be recognized by the input formats that inherit from TextInputFormat, and the correct thing will happen. Is there by chance an error in your log files about codec loading failure.
What version of hadoop are you using, and can you provide a few more details about what input format you are using and how you set the files as input? -- Alpha Chapters of my book on Hadoop are available http://www.apress.com/book/view/9781430219422 www.prohadoopbook.com a community for Hadoop Professionals
