Thank you for the replies.

@ pete: The library is not explicitly written for the DUE. I think I will try your recommended modification.

@ tmd3: I meant of course the range 0...3.3V.

At the moment, the signal is directly (one channel) connected to the analog pin 0 and signal ground to Arduino ground. At first I thought a diode would protect the analog in, since the negative halfwave is cut off, but then of course the FFT is wrong, so lets forget about this.

I am thinking about an input circuit after I found this:

http://www.instructables.com/id/Arduino-Audio-Input/?ALLSTEPS.

Unfortunately my signal source is my smartphone using a freqency generator app and I am working with single sine waves for the beginning.

I will try coupling the audiosignal via voltage divider.

You are right, there is nothing controlling the analogRead frequency, but this doesn't seem to be a problem in the examples I found.

The Radix4_Due library seems to be perfect, it also has a constant sampling rate (48kHz) and works with the DUE. But I just can't find more information about it than on this page

https://coolarduino.wordpress.com/2014/03/11/fft-library-for-arduino-due-sam3x-cpu/ and in the library itself.

The example runs, but only at a buffer size of 2048. If I try to change it in the libraries, the DUE does nothing.

So the question should be now, how to work with the Radix4_Due library and change the array size.

Edit: circuit is a voltage divider with 2x10k and signal coupling with 100nF. Average voltage then is 1,637V and my smartphone puts out ~0,165V AC.

Using the example from the Radix4_Due, it outputs this buffer at 3,5kHz (plotted in excel):

In detail it looks like this (point at the middle, samples 1000...1050):

The FFT looks like this:

.

That means it is correctly working and the input circuit does well.

And now the same thing for 256 array size...