BACKGROUND: Y chromosome microdeletion is one of the major causes of male infertility, and obtaining mature spermatozoa in complete azoospermic factor (AZF)b deletion cases is difficult because germ cells maturation has arrested. However, there are very few reports on spermatogenesis in partial deletions of the AZFb region. We herein report a case of partial AZFb deletion in which sperm were successfully recovered by microdissection testicular sperm extraction (micro-TESE). CASE DESCRIPTION: A 34-year-old man with cryptozoospermia was referred to Reproduction Center, Yokohama City University Medical Center. Both testicular sizes were normal, and the seminal tract had no abnormalities. Serum testosterone and follicle-stimulating hormone levels were also normal. The karyotype was 46,XY, and the Y chromosomal microdeletion test showed no amplification of the sequence-tagged site marker sY1024, which is the proximal part of the AZFb region. We performed micro-TESE, and subsequently identified and cryopreserved many malformed immotile spermatozoa. Intracytoplasmic sperm injection was performed using frozen-thawed testicular sperm that showed slight mobility, but the embryos rarely reached the good blastocyst stage. Although two frozen-thawed embryo transfers were performed, no pregnancies resulted. CONCLUSIONS: In cases of partial AZFb deletion, spermatogenesis may be preserved, and surgical sperm retrieval should be considered even in cases of azoospermia.