Arduino Uno ADC behavior in free running mode I'm using my ATmega328P to sample an analog signal in free running mode. The ADC clock frequency is set to ÷128. I've read that a single analog conversion lasts 13 clock cycles. I would like to know if the number of clock cycles changes if I make the ADC trigger an interrupt after every conversion (ADIE bit set to one). Or will the ADC still use 13 clock cycles and start again on the 14th?

If ADIE is set to zero (no interrupts) will the result of the conversion still be written to ADCL and ADCH? And at what time of the 13 clock cycles is this result written to those registers? This is important to me so I can calculate how much time I have to read those registers.

Would it be possible to set ADIE to zero and instead use a timer interrupt to read ADCL and ADCH every ~1 millisecond. Or am I missing something important?
You may want to take a look at Amanda Ghassaei's tutorials on Arduino DSP techniques or the FFT/FHT code at the Open Music Labs. Both use the Arduino ADC in free running mode. Amanda's code uses interrupts, the Open Music Lab code sits in a tight loop waiting for the conversion to complete.

Based on the Open Music Lab code I can say, yes, the conversion is still written to ADCL and ADCH regardless of the interrupt setting in ADIE. I can't tell from your question how concerned you are about cycle counts, but I don't think you'd see a significant change using interrupts (I'd expect it to be zero). But using interrupts you'll take a hit as you enter and return from the ISR.

As I mentioned in the comment, take a look at Amanda Ghassaei's code. She toggles pin 12 which creates a spike in the trace if you have a scope attached to pin 12 (or a logic analyzer). That will give you a very easy way to determine the actual time to handle the conversion.