This paper proposes a novel heterodyne multiband multiple-input multiple-output (MIMO) receiver with baseband automatic gain control (AGC) for cognitive radios. In the receiver, the analog baseband AGC is introduced to avoid the baseband signals exceeding the voltage reference of analog-to-digital converters (ADCs). This paper proposes a novel technique to estimate the analog devices imperfection in the heterodyne multiband MIMO receiver with the baseband AGC. The proposed technique does not require any high precision analog devices. The performance of the proposed receiver is verified by using computer simulations. As a result, the required resolution of the ADC is nine bits in the proposed receiver. Moreover, the proposed receiver has less computational complexity than that with the baseband interference cancellation unless a frequency band is changed once in nine packets or less.