Is there an association between sex chromosome disomy and semen concentration, motility and morphology? Higher rates of XY disomy were associated with a significant increase in abnormal semen parameters, particularly low semen concentration. Although some prior studies have shown associations between sperm chromosomal abnormalities and reduced semen quality, results of others are inconsistent. Definitive findings have been limited by small sample sizes and lack of adjustment for potential confounders. Cross-sectional study of men from subfertile couples presenting at the Massachusetts General Hospital Fertility Clinic from January 2000 to May 2003. With a sample of 192 men, multiprobe fluorescence in situ hybridization for chromosomes X, Y and 18 was used to determine XX, YY, XY and total sex chromosome disomy in sperm nuclei. Sperm concentration and motility were measured using computer-assisted sperm analysis; morphology was scored using strict criteria. Logistic regression models were used to evaluate the odds of abnormal semen parameters [as defined by World Health Organization (WHO)] as a function of sperm sex chromosome disomy. The median percentage disomy was 0.3 for XX and YY, 0.9 for XY and 1.6 for total sex chromosome disomy. Men who had abnormalities in all three semen parameters had significantly higher median rates of XX, XY and total sex chromosome disomy than controls with normal semen parameters (0.43 versus 0.25%, 1.36 versus 0.87% and 2.37 versus 1.52%, respectively, all P< 0.05). In logistic regression models, each 0.1% increase in XY disomy was associated with a 7% increase (odds ratio: 1.07, 95% confidence interval: 1.02-1.13) in the odds of having below normal semen concentration (<20 million/ml) after adjustment for age, smoking status and abstinence time. Increases in XX, YY and total sex chromosome disomy were not associated with an increase in the odds of a man having abnormal semen parameters. In addition, autosomal chromosome disomy (1818) was not associated with abnormal semen parameters. A potential limitation of this study, as well as those currently in the published literature, is that it is cross-sectional. Cross-sectional analyses by nature do not lend themselves to inference about directionality for any observed associations; therefore, we cannot determine which variable is the cause and which one is the effect. Additionally, the use of WHO cutoff criteria for dichotomizing semen parameters may not fully define fertility status; however, in this study, fertility status was not an outcome we were attempting to assess. This is the largest study to date seeking to understand the association between sperm sex chromosome disomy and semen parameters, and the first to use multivariate modeling to understand this relationship. The findings are similar to those in the published literature and highlight the need for mechanistic studies to better characterize the interrelationships between sex chromosome disomy and standard indices of sperm health. This work was supported by grants from NIOSH (T42 OH008416) and NIEHS (R01 ES009718, P30 ES000002 and R01 ES017457). The authors declare no competing interests. At the time this work was conducted and the initial manuscript written, MEM was affiliated with the Environmental Health Department at the Harvard School of Public Health. Currently, MEM is employed by Millennium: The Takeda Oncology Company. N/A.