This study aimed to examine whether the vomeronasal organ (VNO) is a prerequisite in mice to acquire essential information from various social odors and whether long-term VNO dysfunction can elicit behavioral and physiological changes in mice. We used binary choice tests and habituation-dishabituation tests to measure the abilities of male mice to recognize social odors. We found that males with the VNO ablation failed to show olfactory preferences between the odors of mate versus non-mate females, offspring versus non-offspring pups, or oppositesex conspecifics versus predators (cats or rats), but were capable of discriminating between the two treatments in each of the paired odors, suggesting that male mice with VNO ablation might smell out the chemical differences of the two types of odors, but could not extract the biological information contained in the odors. Furthermore, prolonged VNO deficiency resulted in a reduction in crossing behavior in a light/dark box, the frequency of urine marking, and the time spent in the center in an open field. These results indicate that chronic VNO dysfunction led to anxiety-like or submissive behavior. In addition, males with VNO ablation had atrophic adrenal glands and hypertrophic preputial glands, suggesting that VNO dysfunction could damage the physiological conditions to buffer the stress and that pheromone perception deficiency might enhance self-odor production in mice.