Objective: To investigate the toxic effect of HIV-1 Vpr protein on neurons. Methods: HIV-1 vpr gene was amplified by nested PCR in four parts of peripheral spleen (SPL) and central nervous tissue meninges (MG) of HIV-associated dementia (HAD) patients and non-HAD patients. Eukaryotic expression vector pEGFP-N1-vpr was constructed. The gene sequence and key amino acid sites were analyzed by BLAST and MEGA6. The expression of Vpr protein in N2a cells was detected by Western-blotting. The effects of Vpr proteins from different sources on the activity and cell cycle of N2a cells were studied by flow cytometry. Results: HIV-1 vpr gene was successfully amplified by PCR. Sequence analysis showed that the vpr gene sequence belonged to HIV-1B subtype. There were amino acid mutations at C-terminal 84, 86 and 87 sites of central Vpr protein from HAD and non-HAD patients. Vpr protein could inhibit the activity of nerve cells, leading to G2 phase arrest. Different sources of Vpr had different intensity of action. Compared with other groups, Vpr protein from the meninges of HAD patients showed stronger inhibition of cell activity and G2 phase arrest ability. Conclusions Variations in key amino acid sites of Vpr protein could cause significant changes in its biological functions, and its significance in the pathogenesis of HAD remains to be further studied.