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Thanks for your help, JavaPF. I will mark my threads when they are solved from now on.

I can't believe I didn't see this. It seems so obvious now. I thought that the loop condition just verified that the first line was not null and then the read the first line again for the printing,...

The input file was a file I used to test if it would work that contained the following:
AA
BB
CC
DD
What was printed in the output file was:
BB
DD
Here is the code:

I'm trying to write my first I/O program and I seem to have a problem with using the BufferedReader class. Every time I read in from a .txt document and then print out to a different one it prints...