A method and system is provided for determining noise components of an analog-to-digital converter. In one aspect of the invention, a method comprises providing an input signal to a signal input and a clock input of the ADC, outputting a plurality of samples at a sampled phase on the input signal for a plurality of sampled phases, and determining a jitter noise factor value, a reference noise factor value, and a total noise spectrum based on the plurality of samples for each of the plurality of sampled phases. A least means square algorithm is performed on the plurality of jitter noise factor values, reference noise factor values, and total noise spectra to estimate at least one of a jitter noise component and a reference noise component.