We investigated whether the presence of Y chromosome azoospermia factor (AZF) microdeletions impacts upon the outcomes of intracytoplasmic sperm injection (ICSI) using fresh ejaculated spermatozoa. Sixteen oligozoospermia patients with Y chromosome AZFb or AZFc microdeletions and undergoing ICSI cycles between March 2013 and November 2014 were studied. Twenty-six infertile men with normal Y chromosomes and also undergoing IVF/ICSI in the same time period were used as controls. A retrospective case-control study approach was used. Among the 16 cases, 12 (75%, 12/16) had deletions of AZFc markers (sY152, sY254 and sY255), one (6.25%, 1/16) had a deletion of sY152, and two (12.5%, 2/16) had deletions of sY152, sY254, sY255 and sY157. AZFb microdeletions were found in one patient (6.25%, 1/16). There were no significant differences between groups for cleaved embryo rate, high-grade embryo rate, blastocyst formation rate, embryo implantation rate, clinical pregnancy rate and delivery rate. The clinical outcomes of ICSI for oligozoospermic patients with Y chromosome AZF microdeletion are comparable to those of infertile patients with normal Y chromosomes. Our findings indicate that ICSI should be offered to patients with an AZFc deletion and that oligozoospermia patients with AZFb microdeletions are likely to father children.