Bacteria can be isolated from most seminal fluid samples, but the significance of these microorganisms is uncertain because most men lack symptoms associated with bacterial infection of the reproductive tract. We obtained semen samples from 37 men attending a Special Infertility Clinic and assessed the relationship between seminal fluid microorganisms and seminal fluid analysis including sperm motility, morphology, and concentration; the numbers of polymorphonuclear leukocytes and other white blood cells; and the hamster zona-free oocyte sperm penetration assay. Aerobic and/or anaerobic bacteria were recovered from 36 of the 37 samples. One hundred eighty-eight isolates (113 aerobes, 74 anaerobes, and one yeast) were recovered, with a mean of 5.2 isolates per semen specimen. The microorganisms recovered from the samples included: coagulase-negative staphylococci (89%), viridans streptococci (65%), diphtheroids (86%), Peptostreptococcus sp (62%), Bacteroides sp (27%), Gardnerella vaginalis (19%), Lactobacillus sp (16%), Actinomyces sp (16%), Enterococcus (11%), and Veillonella (11%). Other microorganisms including group B streptococcus, Hemophilus, Escherichia coli, Mobiluncus, and Clostridium were each recovered from fewer than 10% of the specimens. When the microbiology of seminal fluid specimens with or without polymorphonuclear leukocytes was compared, the presence of polymorphonuclear leukocytes in the semen was not associated with the isolation of staphylococci (33 versus 25%), viridans streptococci (33 versus 28%), Bacteroides sp (17 versus 37%), or Peptostreptococcus (31 versus 33%) (P greater than .05 for each comparison). The proportion of semen samples yielding bacterial isolates was similar after categorization by normal motility (more than 60%), pyospermia (six or more leukocytes per 100 sperm), sperm concentration, morphology, and a normal sperm penetration assay (11% or more).(ABSTRACT TRUNCATED AT 250 WORDS)