Background: We showed that in men with a constitutional chromosomal abnormality, DNA fragmentation was significantly higher in chromosomally unbalanced spermatozoa than in spermatozoa with a normal or balanced chromosomal content. These results could be explained by a phenomenon already described in infertile men: abortive apoptosis. Objectives: To determine if magnetic-activated cell separation could select spermatozoa with lower levels of DNA fragmentation and unbalanced chromosome content in men carrying a structural chromosomal abnormality. Materials and methods: The spermatozoa of ten males with a chromosomal rearrangement were separated into two populations using MACS (annexin V (-) and annexin V (+) fractions), in order to study meiotic segregation by FISH, the percentage of spermatozoa with an externalization of phosphatidylserine (EPS) by annexin V staining and DNA fragmentation by TUNEL on the whole ejaculate and on selected spermatozoa in the same patient. Results: For all patients, the percentage of spermatozoa with EPS decreased in the annexin V (-) fraction and increased in the annexin V (+) fraction as compared to the frozen-thawed semen sample. The rates of DNA fragmentation were statistically much lower in the annexin V (-) fraction when compared to the rate before MACS for all but one patient. Conversely, we observed a statistically significant higher rate of DNA fragmentation in the annexin V (+) fraction for 6 patients. After MACS, there was a significant increase of normal/balanced spermatozoa in the fraction of annexin V (-) for all patients. Conversely, we observed a significant decrease in the fraction of annexin V (+) for seven patients. Discussion and Conclusions: MACS is a promising tool for increasing the selection of healthy spermatozoa, with a decrease in the number of spermatozoa with EPS, DNA fragmentation and chromosome unbalance, for use in assisted reproductive technologies such as ICSI for males with a chromosomal structural abnormality.