Last Revised: April 12, 2024

Revision 4/2018

The requirements in Penn's Chemical Hygiene Plan SOP: Irritants, SOP: Reproductive Health Hazards, and SOP: Carcinogens apply to phenol-chloroform extractions.  The Fact Sheet below gives hazard information and precautions for working with these chemicals; however, this information is provided as a supplement to the SOPs, which must first be read and understood by anyone planning to do phenol-chloroform extractions.


Phenol-Chloroform Extraction is a common laboratory technique used to separate proteins from nucleic acids. An equal volume of phenol:chloroform (50:50) is added to a nucleic acid sample. The mixture is centrifuged to separate the organic and aqueous phases. The organic phase is discarded. Ethyl ether is sometimes used to remove traces of chloroform.

Hazards Associated with Phenol-Chloroform Extraction

Biological Hazards

There are no biological hazards associated with this procedure unless human source materials are used.

Chemical Hazards

Phenol is readily absorbed through the skin and can cause severe burns to the eyes and skin. Phenol has a local anesthetic effect, so that no pain may be felt on initial contact. Systemic effects from prolonged or repeated exposure include damage to the liver and kidneys. Phenol is suspected to cause genetic effects.  

Chloroform is a skin and eye irritant, and it is a suspected human carcinogen and reproductive hazard. Adding chloroform to phenol enhances the ability of phenol to be absorbed by the skin.

Ethyl ether is a mild skin and eye irritant. The primary hazard associated with ethyl ether is that it is extremely flammable and it forms explosive peroxides after prolonged exposure to light and air. When kept for prolonged periods after it has been opened, ethyl ether forms peroxides that may explode when the container cap is removed or when it is concentrated during laboratory activities. See: SOP: Peroxide-Formers, and SOP: Flammable Liquids.

Refer to Safety Data Sheets or contact EHRS for more detailed information on the hazards of these and other laboratory chemicals.

Equipment Hazards

Centrifugation may result in the formation of aerosols and droplets.

Special Work Practices

  • Perform procedures involving phenol, chloroform, and ether in a chemical fume hood.
  • Wash hands thoroughly immediately after working with these chemicals. Never eat, drink, chew gum, apply cosmetics, take medicine or store food in a laboratory where these chemicals are used and stored.
  • Grasp both the tube and the cap when vortexing to prevent the cap from opening, causing a splash or aerosol.
  • Use sealed safety cups when centrifuging phenol:chloroform, and wait at least 10 minutes before opening the centrifuge to prevent exposure to aerosols.

Personal Protective Equipment

Eye Protection

Wear safety glasses when performing phenol:chloroform extraction, even when working in a fume hood.

Phenol can cause severe burns to the eyes. Wear chemical splash goggles when there is a splash hazard (for example, when pouring phenol).


Wear disposable nitrile gloves to protect against accidental hand contact. If accidental contact occurs, remove and discard contaminated gloves immediately. (The breakthrough time for a 4 mil nitrile glove is approximately 3 minutes for chloroform.)

Protective Clothing

Wear standard laboratory apparel. (Lab coat, long pants and closed toe shoes.)


Store ethyl ether in a flammable liquid storage cabinet. Store phenol away from strong oxidizers and store chloroform away from strong alkalis. Store chloroform in a dark location.

Write the date received and the date opened on all containers of ether. Discard open containers of ether within six months of opening.

Waste Disposal

Discard phenol chloroform mixture in a properly labeled waste container.

Discard all syringes used in phenol:chloroform extraction in a sharps container labeled "Mutagen/Carcinogen Sharps Do Not Autoclave."

Place all pipettes that contacted phenol:chloroform in a rigid container and discard as hazardous waste.

Follow the hazardous waste requirements found in the Laboratory Chemical Waste Management Guidelines for labeling, storage, and pick-up requests for chemical containers.


Emergency Contacts

General emergency response information can be found at Emergency Info


General procedures for chemicals spill response can be found in Section X: Chemical Spills in this CHP.

Do not hesitate to call EHRS for assistance with spill cleanup

24 hours: 215-898-4453

Contact Penn Police (511) only if the spill involves a fire, imminent risk of fire, an injury requiring an ambulance, or if there is a hazard that may affect others in the building.