We conducted this study to obtain a comprehensive picture of molecular epidemiology of HIV-1 in three neighboring countries, i.e. Afghanistan, Iran, and Pakistan as a basis for discussing possible hypothesis regarding between-country virus transmission. Our results showed that subtype composition differs between these countries with more variation in Pakistan than Iran and Afghanistan. The CRF35-AD clade was predominant in Afghanistan and Iran while the A1 subtype was predominant in Pakistan. HIV-1 sequences obtained from Pakistan (belonging either to B, A1, or CRF35_AD clades)  did not group with the sequences obtained from Afghanistan and Iran. However, CRF35_AD clades from Afghanistan made two significant clusters with those strains from Iran. The results also showed that CRF35_AD clades from Afghanistan had more diversity than those in Iran suggesting its older presence in this country. Putting these findings together and considering drug trafficking/immigration events from Afghanistan to Iran we hypothesized that HIV epidemics might have been transmitted from Iran to Afghanistan. However, the reverse order might also be true but with less support from the existing evidence. There was no indication of Iran-Pakistan HIV transmission. Performing sophisticated evolutionary analysis is needed to test these hypotheses about the origin and transmission pattern of the virus among these countries.