From the Area51 proposal
Null byte injection depends on a mismatch in the way that strings are handled.
e.g. Java stores the length of the string independently of the content of the string, while C starts at the beginning of the string and checks for a Null Byte to indicate the end of the string.
As a result, Java code can perform checks like "does the file requested end with .jsp" on a string like "/etc/shadow%00.jsp" (where %00 represents the null byte), and return true, while passing this string to "new FileInputStream()" will result in the underlying OS (both Windows and Linux) trying to open "/etc/shadow".
(Relevance of trying to open /etc/shadow on Windows is left as an exercize for the reader :-) )
Null byte injection in filenames was fixed in Java 7 update 40 (released around Sept. 2013). So, its FINALLY fixed.