The study of male infertility after spinal cord injury (SCI) has enhanced the understanding of seminal plasma (SP) as an important regulator of spermatozoa function. However, the most important factors leading to the diminished sperm motility and viability observed in semen of men with SCI remained unknown. Thus, to explore SP related molecular mechanisms underlying infertility after SCI, we used mass spectrometry-based quantitative proteomics to compare SP retrieved from SCI patients to normal controls. As a result, we present an in-depth characterization of the human SP proteome, identifying ϳ2,800 individual proteins, and describe, in detail, the differential proteome observed in SCI. Our analysis demonstrates that a hyper-activation of the immune system may influence some seminal processes, which likely are not triggered by microbial infection. Moreover, we show evidence of an important prostate gland functional failure, i.e. diminished abundance of metabolic enzymes related to ATP turnover and those secreted via prostasomes. Further we identify the main outcome related to this fact and that it is intrinsically linked to the low sperm motility in SCI. Together, our data highlights the molecular pathways hindering fertility in SCI and shed new light on other causes of male infertility. Molecular & Cellular Proteomics 15: 10.1074/mcp.M115.052175, 1424-1434, 2016.For many years, seminal plasma (SP) 1 , the liquid component of semen, was believed to have a single and simple physiological significance as the carrier of spermatozoa through both male and female reproductive tracts. It was around 50 years ago when the compositional complexity of this fluid started to be investigated, demonstrating that SP not only aids in cellular transport but also provides energy and metabolic support to the transiting spermatozoa (1, 2). Today, growing evidence indicates that SP plays a role far beyond what was once envisioned, including acting as an essential regulator of spermatozoa function contributing to (enabling/ hindering) the cellular ability of fertilization (3). Composed of secretions derived from the testis, epididymis and male accessory glands (prostate, seminal vesicles and bulbourethral glands), SP is a mixture of sugars, inorganic ions, organic salts, (phospho)lipids and proteins (4). Such a heterogeneous composition emphasizes the complex biochemical cascades triggered within SP during, and immediately after, ejaculation and defines the beneficial and/or detrimental nature of SP in the overall reproductive process (5). From a clinical point of view, studies have confirmed the participation of SP in the etiology of male infertility. By studying semen of men with spinal cord injury (SCI), who become infertile after a traumatic injury and often present with an unusual seminal profile characterized by normal sperm concentration but extremely impaired sperm motility and viability, Brackett et al. demonstrated how SP can impair sperm function leading to infertility (6). Specifically, the authors mixed SP obtained from ...