In a non-ideal PLL circuit, leakage of the reference signal into the control line produces spurious tones. When the distorted PLL signal is used in an analog-to-digital converter (ADC), it creates spurious tones in the sampled data as well. This paper analyzes this effect and proposes a solution to remove the leakage effects. The algorithm estimates the jitter errors from the spurious sidebands and provides a way to compensate the distorted sampled data in the digital domain.