In this paper we propose a generally applicable frequency domain equalization and radio frequency (RF) impairment compensation technique for orthogonal frequency division multiplexing (OFDM) based multi-input multi-output (MIMO) systems. RF impairments such as in-phase quadrature-phase (IQ) imbalance and carrier frequency offset (CFO) are unavoidable in low-cost analog front-end systems, but can result in a severe performance degradation. In this paper, a digital compensation scheme is developed for joint transmitter and receiver IQ imbalance along with front-end filter mismatch, CFO and frequency selective channel distortions in OFDM based MIMO systems. This scheme can also be extended for the multi-user scenario where each user signal suffers from a different frequency offset along with IQ imbalance.