Chronic mountain sickness (CMS) is a condition in which the hematocrit is increased above the normal level in residents at high altitude. High altitude polycythemia (HAPC) is the most characteristic sign of CMS. However, the pathogenesis of HAPC is poorly understood. The present study aimed to investigate the gene expression profile of HAPC in Han Chinese migrating to the Qinghai-Tibetan Plateau and to identify the pathogenetic mechanisms. A total of 9 differentially expressed genes were identified in HAPC patients using microarrays: 5 were up-regulated and 4 were down-regulated. Functional analysis of the array data revealed that cell division cycle 42 (CDC42) and the human immune response may be key features underlying the mechanism and development of HAPC.