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    <p>You shouldn't write to the output file before the actual encryption process. The <code>CryptoStream</code> will handle all the necessary padding when it is closed. Also the for loop isn't necessary as the inner while loop will read the entire file. Also you should only write as much as was read from the file. Try these changes.</p> <pre><code>private static void Enc(string decryptedFileName, string encryptedFileName) { PasswordDeriveBytes passwordDB = new PasswordDeriveBytes("ThisIsMyPassword", Encoding.ASCII.GetBytes("thisIsMysalt!"), "MD5", 2); byte[] passwordBytes = passwordDB.GetBytes(128 / 8); using (FileStream fsOutput = File.OpenWrite(encryptedFileName)) { using(FileStream fsInput = File.OpenRead(decryptedFileName)) { byte[] IVBytes = Encoding.ASCII.GetBytes("1234567890123456"); RijndaelManaged symmetricKey = new RijndaelManaged() { Mode = CipherMode.CBC,Padding=PaddingMode.Zeros}; ICryptoTransform encryptor = symmetricKey.CreateEncryptor(passwordBytes, IVBytes); using (CryptoStream cryptoStream = new CryptoStream(fsOutput, encryptor, CryptoStreamMode.Write)) { byte[] chunkData = new byte[chunkSize]; int bytesRead = 0; while ((bytesRead = fsInput.Read(chunkData, 0, chunkSize)) &gt; 0) { cryptoStream.Write(chunkData, 0, bytesRead); //KEY FIX } } } } } </code></pre> <p>[edit]</p> <p>Oh I've missed out on a lot of information. I misread what your sizes were thinking 140,912 was the size, not difference. Now that I see that, I can make more intelligible response. Based on your code, the difference in sizes should be comparable to your chunk size. Since the chunkSize can be somewhat large, your code will typically write up to chunkSize more data than is actually in your input file (as Greg and caf pointed out). The line that I've marked is <em>the</em> reason for the discrepancy.</p>
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    1. COCan you explain why I cant write to the stream before the encryption? The data I'm writing right at the start (the first 24 bytes) doesn't want to be encrypted, as I need it to unencrypt the rest. It actually doesn't seem make any difference if I use chunkSize, or bytesRead, as any unused bytes in the chuckData array are just null, and don't seem to get encoded by the cryptoStream.Write() method anyway. If this wasn't the case, wouldn't this surely negatively affect encryption / decryption process, which works perfectly fine?
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    2. COAs for writing to the file before the encryption, I suppose that would be fine. Just that you need to remember that if you try to decrypt, you need to offset past these written bytes to properly decrypt the data. It really shouldn't affect the encryption process but does the decryption. I'll update my answer to directly address what seems to cause the problem.
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    3. COSorry, I'll have to think about it. I thought I would have a reasonable explanation but don't at the moment (and I'm pressed for time). I've helped another person with pretty much the same exact problem but never heard back on the final result. I'll get back to you on this.
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