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Purpose: To compare the frequency of chromosomal heteromorphisms in reproductive failure and fertile control individuals in Northeast China, and investigate the impact on reproductive failure Methods: 1751 males and 1424 couples with reproductive failure ( n = 4599) and 777 fertile control individuals in Northeast China were enrolled. Chromosome karyotype analysis was performed on peripheral blood lymphocytes with standard G-banding. Additionally, C-banding was performed with heterochromatin heteromorphisms, and NORs-banding with satellites/stalks variations. Multiplex polymerase chain reaction (PCR) adopted for the amplification using nine specific sequence tagged sites (STS) were used to detect Y-chromosome microdeletions with Y chromosome variations (Yqh±). At the same time, 38 heteromorphic probands' family members were recalled for performing karyotype analysis and to be surveyed for their detailed reproductive history. Results: The frequency of chromosomal heteromorphisms in reproductive failure patients (2.74 %, 126/4599) was of no statistically significant difference as compared with fertile control individuals (2.06 %, 16/777) ( P > 0.05). Eight cases of Y variation (Yqh±) probands with Y-chromosomal microdeletions were detected among 44 reproductive failure patients and 6 fertile control men. In the 38 recalled families, the probands of fathers or mothers, even some of their brothers or sisters, had the same heteromorphic karyotypes as probands' despite that they didn't have any adverse reproductive history. Conclusions: There was no statistically significant difference in frequency of chromosomal heteromorphisms between reproductive failure and fertile control individuals in Northeast China. Males with Y variations (Yqh±) should be ordered Y-chromosomal microdeletions detection. Through the analysis of 38 recalled families, we can also conclude that chromosomal heteromorphisms were not the impact factors for reproductive failure. [ABSTRACT FROM AUTHOR]