The aim of this study was to evaluate thymus function in mice with hypertension. A total of 60 C57BL/6J mice were randomized into control, sham surgery and two-kidney, one-clip groups (n=20 in each). At 4 or 8 weeks after surgery, mice were sacrificed, and blood, spleens, kidneys and thymuses were harvested. The results of reverse transcription-quantitative polymerase chain reaction analysis revealed that the mRNA levels of Forkhead box protein N1 (Foxn1) and autoimmune regulator (AIRE) in the thymus tissue of mice from the HTN group were significantly lower than those from the control group at 4 and 8 weeks (P<0.05). Foxn1 and AIRE expression was also reduced in the sham surgery group at 4 weeks after surgery, but had recovered 4 weeks later. Similar results were observed for the expression of signal-joint T cell receptor excision circles and the percentages of T cell subsets. The present study indicates that impaired thymus function is associated with hypertension in mice, which suggests that thymus function may be a novel target for the treatment of patients with hypertension.