Infertility is a serious problem that affects between 10%-15% of couples all over the world in which half of these cases are attributed to males. Deletions in the azoospermia factor (AZF) of the Y chromosome have been investigated and shown to be associated with azoospermia and severe oligozoospermia in many populations. However, the percentages of microdeletions were somehow variable. The purpose of this study was to investigate the association between microdeletions in the AZF region of the Y chromosome and infertility among male Jordanians.A total of 65 oligoozospermic and non-obstructive azoospermic infertile men (Study group) and 20 fertile men (control group) were investigated for microdeletions in the AZF using multiplex PCR. We found one out of 65 (1.5%) had Y microdeletions. Microdeletions were detected in the AZFb and AZFc regions. The percentage of Y chromosome microdeletions in Jordanian infertile males is considered low compared to that from other countries. We also report a molecular genetic characterization of a sex-reversed 46,XX male, a very rare genetic abnormality in humans