The objective of this study was to determine the potential hazardous effects of sorting process by flowcytometry on the quality of boar spermatozoa by flowcytometer. Freshly collected boar semen was diluted and divided into two groups; control none sorted and sorted. Sperms in sorted group were processed with flowcytometer for cell sorting with 100 uM nozzle under the 20 psi pressure. Measurements on each parameter were made at two time points, 0hr (right after sorting) and 24 hr post sorting. Although there was a tendency of lower viability in sorted group than none sorted control group, the percentage of live cells in control(75.83+-6.92 & 59.53+-10.34) was not significantly different from sorted (59.7+-7.34 & 43.97+-3.76) at both 0 and 24 hr post sorting. However, sorted sperm showed significantly lower mitochondrial function compared to the control at both 0 h (79.37+-3.22 vs. 63.50+-10.05) and 24hr(67.27+-3.22 vs. 46.97+-5.37) time points (p<0.007). Sperm DNA fragmentation rate was significantly lower in control (22.0+-7.04) than that of sorted (32.27+-7.49) at 24 hr time point (p<0.0002). Taken together, these data suggested thatsorting process by flowcytometer may have influenced sperm motility rather than viability. Also high speed sperm sorting by flowcytometer has significant effects on DNA fragmentation on elapsed time after sorting.