Interference alignment (IA) is an effective technique to eliminate the interference among wireless nodes. In a multiinput multi-output (MIMO) cognitive radio system, multiple secondary users can coexist with the primary user without generating any interference by using the IA technology. However, few works have considered the fairness of secondary users. In this paper, not only is the interference eliminated by IA, but also the fairness of secondary users is considered by two kinds of algorithms. Without losing generality, one primary user andKsecondary users are considered in the network. Assuming perfect channel knowledge at the primary user, the interference from secondary users to the primary user is aligned into the unused spatial dimension which is obtained by water-filling among primary user. Also, the interference between secondary users can be eliminated by a modified maximum signal-to-interference-plus-noise algorithm using channel reciprocity. In addition, two kinds of fairness algorithms, max-min fairness and proportional fairness, among secondary users are proposed. Simulation results show the effectiveness of the proposed algorithms in terms of suppressed interference and fairness of secondary nodes. What is more, the performances of the two fairness algorithms are compared.