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Atomic force microscopy (AFM) has been employed to examine morphological and topographical changes caused by human immunodeficiency virus (HIV) and the effects of highly active antiretroviral therapy (HAART) on spermatozoon of HIV infected patients. This powerful technique has allowed us to visualize morphological alterations present in the spermatozoa of patients either with or without treatment. In addition to this, even the minute details, such as viral particles, located on the membrane of the spermatozoa, and the merging of such particles on the surface of the spermatozoa were detected with precision. The most important aspect is that AFM, unlike electron microscopy, permits to image virions in their nearly natural environment. Excess of damage of spermatozoon is due to the chemicals involved in HAART rather than the damage made by virus.