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This paper describes experimental approaches to analyze the effect of the substrate noise on phase-locked loop (PLL) performance. Spectral analysis considering noise transfer functions of the PLL is used to identify the substrate-noise sensitive components of the PLL. Analyzing the sidebands seen in a spectrum analyzer confirms the importance of knowing the PLL loop dynamics and noise transfer functions. It also leads to the conclusion that the PLL blocks other than the VCO can be more sensitive to substrate noise coupling, depending on the substrate noise frequency. Furthermore, the result shows that intermodulation near the reference clock frequency could be a dominant source of generating sidebands in fractional-N PLLs.