Background: Cholesterol is essential for cell membrane stability, permeability, and fluidity. Cholesterol is present in seminal plasma, but whether a relationship between the level of cholesterol in seminal plasma and semen quality exists remains to be elucidated. Objectives: To explore the association between cholesterol levels in seminal plasma and serum cholesterols, semen quality, and serum reproductive hormones. Secondly, to explore whether the associations are biologically plausible. Materials and Methods: An association study between cholesterol levels in seminal plasma and semen quality in 403 men, median age 19 years, from the general population. Additionally, an immunohistochemical evaluation of proteins involved in cholesterol metabolism and transport in tissues from the male reproductive tract (testis, epididymis, prostate, and seminal vesicle). Tissue specimens were investigated by immunohistochemistry for markers of cholesterol metabolism and transport (ABCA1, ABCG1, CYP11A1, CYP51A1, HMGCR, LAL, LCAT, LDLR, and SOAT1). Results: Trend analyses showed that total amount of total cholesterol in seminal plasma was positively associated with sperm concentration, total sperm count, sperm motility, and morphology (all p < 0.008, adjusted). Cholesterol concentrations in seminal plasma were neither associated with serum cholesterol and lipid levels nor serum reproductive hormone (FSH, LH, testosterone, estradiol, sex-hormone-binding globulin, inhibin b) levels. All investigated markers of cholesterol metabolism and transport were expressed in the investigated tissue specimens to varying degrees. Discussion: Seminal plasma level of cholesterol was positively associated with semen parameters. The presence of proteins and enzymes involved in cholesterol metabolism in Leydig cells, Sertoli cells, and maturing germ cells in the seminiferous tubules supports the view that cholesterol may be important for spermatogenesis. Conclusion: Cholesterol level in seminal plasma may be an indicator of semen quality. Investigations are needed to corroborate or refute our findings and to clarify the exact role of cholesterols for semen quality.