Bacteriophage-encoded toxins (e.g. botulism toxin, diphtheria toxin, cholera toxin, and Shiga toxin) are secreted polypeptides that modulate the virulence of the host bacteria. Exotoxin genes carried by bacteriophages are responsible for many of the symptoms associated with human diseases.
Expression of any virulence factor can benefit the bacterium host, the bacterial population, and the encoding phage/prophage 
.
Bacteriophage-encoded exotoxins
Source:Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved .
| Virus | Host bacteria | Virulence factor | Gene | Type | Disease (third eukaryotic organism) |
| β-phage | Corynebacterium diphtheriae | Diphtheria toxin | tox | Exotoxin | Diphteria |
| Phage C1 | Clostridium botulinum | Neurotoxin | C1 | Exotoxin | Botulism |
| Phage H-19B, Enterobacteria phage 933W | Escherichia coli | Shiga toxin 1A, 1B, 2A, 2B | stx1AB stx2AB |
Exotoxin | Dysentery |
| Phage CTXΦ | Vibrio cholerae | Cholera toxin A, B | ctxAB | Exotoxin | Cholera |
| Phage ΦC3208 | Escherichia coli | Hemolysin | hly2 stx2AB |
Exotoxin | Hemolysis |
| Phage ΦCTX | Pseudomonas aeruginosa | Cytotoxin | ctx | Exotoxin | Cytotoxicity (especially on leukocytes) |
| Phage N315 | Staphylococcus aureus | Enterotoxin P | sep | Exotoxin | Vomiting |
| Phage Mu50A | Staphylococcus aureus | Enterotoxin A | sea | Exotoxin | Food poisoning syndrome |
| Phage Φ13 | Staphylococcus aureus | Enterotoxin A | entA | Exotoxin | Gastroenteritis |
| Phage ΦETA | Staphylococcus aureus | Exfoliative toxin A | eta | Exotoxin | Scaled-skin syndrom |
| Phage ΦPVL | Staphylococcus aureus | Panton-Valentine leukocidin S, F | lukS | Exotoxin | Leukocytes destruction |
| Phage T12 | Streptococcus pyogenes | Toxin A | speA | Exotoxin | Scarlet fever |
| Phage CS112 | Streptococcus pyogenes | Toxin C | speC | Exotoxin | Scarlet fever |