Objective To report the cytogenetic and molecular genetic analysis of the first two cases of non-chimerism and chimerism karyotype in Chinese male patients who suffer from azoospermia, which may be caused by pseudo dicentric Y chromosomes. Design Case study. Setting Academic reproductive medicine center. Patients Two male patients with azoospermia, carrying pseudo dicentric Y chromosome.Interventions Review the records of inquiry, testicular biopsy, pathological examination, semen routine examination, endocrine evaluation, cytogenetic chromosomal analysis, and FISH detection of peripheral blood to evaluate Y chromosome deletion. Main outcome measures To investigate the possible association among pseudo dicentric Y, chimeric status and azoospermia. Results Two patients were both diagnosed with azoospermia by a variety of andrology inspections. Further chromosomal analysis and FISH indicated their pseudo dicentric Y chromosome and different chimerism status. PCR confirmed simultaneous deletions of AZFb and AZFc regions in the Y chromosome of both patients. Conclusions Pseudodicentric Y chromosome affecting the long arm may lead to a male phenotype by duplicating the sex-determining region of Y chromosome (SRY) fragment and chimeric status may further impact patient's hormone levels, which obstruct spermatogenesis. However, the deletion of the azoospermia factor (AZF) is likely the key factor that causes azoospermia.