The interesting condition of brown-colored semen has often been observed during assisted ejaculation of men with spinal cord injury (SCI). This condition has not been reported in the literature, and its cause is unknown. To investigate this condition, the present study examined the incidence and quality of brown semen and its relationship to level of SCI, time since SCI, number of successive ejaculations, ejaculation frequency, and ejaculation method in a total of 664 semen specimens from 162 SCI men. In addition, a microscopic evaluation was performed on brown semen specimens from SCI men, not-brown specimens from SCI men, and normally colored specimens from normal men. The results showed that 27% of SCI subjects had brown semen on at least one ejaculation. There was no difference between men producing and men not producing brown semen in age, level of injury, or years postinjury. The duration of an ejaculation, number of successive ejaculations, and frequency of ejaculation were not associated with occurrence of brown semen. Sperm concentration and sperm motility were not significantly different in brown and not-brown specimens. Specimens from subjects who produced brown semen had similar pH but lower volume than specimens from subjects who did not produce brown semen. Brown semen had a thin consistency more often than not-brown semen. Brown specimens contained intact red blood cells (RBCs) and/or heme pigment more often than not-brown specimens; however, one half and one third of the specimens, respectively, contained neither RBCs nor heme pigment. The cause of brown semen is unknown but may relate to seminal-vesicle dysfunction.