This paper uses multitone signals to simplify the analysis of 3 × 3 multiple-input multiple-output (MIMO) Volterra systems by isolating the third-order kernel outputs from each other. Multitone signals fed to an MIMO Volterra system yield a spectrum that is a permutation of the sums of the input signal tones. This a priori knowledge is used to design multitone signals such that the third-order kernel outputs are isolated in the frequency domain. The signals are designed by deriving the conditions for the offset and spacing of the input frequency grids. The proposed technique is then validated for the six possible configurations of a 3 × 3 RF MIMO transmitter impaired by crosstalk effects. The proposed multitone signal design is used to extract the third-order kernel outputs, and their relative contributions are analyzed to determine the dominant crosstalk effects for each configuration.