How to Clean Your Rotary Evaporator

By Aimee O'Driscoll, 16 December 2019

A rotary evaporator is a complex piece of equipment with multiple components. As such, it’s definitely not the simplest item in the lab to clean. However, it’s important to clean your rotary evaporator properly. Leaving residue in its components could pose safety risks or affect the outcome of subsequent applications.

There are two main ways to clean your rotary evaporator glassware, both of which we’ll discuss further below, including their pros and cons:

  1. The “quick and dirty” method: This involves a quick flush with acetone or another solvent.
  2. Thorough cleaning of glassware: In this case, you need to dismantle the apparatus before cleaning.

In either case, you should aim to clean the rotovap soon after you finish using it. This avoids residue drying onto the glassware and making it more difficult to clean.

1. The “Quick and Dirty” Method

You may have heard about a fast and simple method to clean your rotary evaporator glassware using a quick flush with acetone. The video below illustrates how this is done, but here are the general steps:

  • Fill a small to medium-sized two-neck round-bottom flask about halfway with acetone. (A three-neck flask with a stopper in one socket will work too.)
  • Connect one socket to the rotovap (where the evaporation flask would usually go). You can secure it in place or hold it with one hand. Note, the flask should not be set to spin during this process.
  • Use your thumb to close the second socket of the two-neck flask.
  • Set the vacuum pump to around 250 mbar and switch it on. You should start to see the acetone boil as a result of the reduced pressure.
  • Quickly remove your thumb from the socket and you’ll see acetone shoot through the rotovap.
  • Close the socket with your thumb again and repeat the flush if needed.



The obvious advantage to this method is that it’s very fast. You don’t even need to dismantle your setup. However, it could potentially cause problems. The rapid suction of the solvent into the system means you could up with solvent in your vacuum pump. If this gets into the oil of an oiled pump, it will decrease the time you’ll have between oil changes. If you’re using an oil-free pump such as a membrane pump, it could become flooded with solvent. If this happens, you’ll need to keep it running to help clear the solvent and dry it out. 

In either case, in the long run, you’re better off skipping this cleaning method altogether and dismantling your setup for cleaning instead.

2. Thorough Cleaning of Glassware

The proper way to clean your rotary evaporator is to take it apart and wash each piece separately. Removable and washable parts include the evaporation flask, condenser, collection flask, and vapor tube. 

Many manufacturers will provide advice about cleaning a specific rotary evaporator’s components, but these are the basic steps:

  1. Ensure parts are adequately cooled (chilled condensers should be at room temperature).
  2. Remove the component and dispose of its contents according to regulations.
  3. Flush the component with an appropriate solvent. If necessary and suitable as per manufacturer specifications, you can use a brush to remove more stubborn residue. 
  4. Allow components to dry before reassembly.

Depending on your application, you may wish to sterilize your glassware using an autoclave. Just bear in mind that if you’re using safety-coated glassware, there may be some restrictions on what settings you use and how long you autoclave for. In particular, you should avoid sudden changes in pressure as this can cause the coating to come away from the glassware, leaving folds and creases in the coating once the glassware cools.

Cleaning Other Parts of a Rotary Evaporator

Aside from the glassware, you need to keep up with regular cleaning of other parts of the rotary evaporator.

  • The exterior of the rotovap unit: Cleaning the outside of the rotary evaporator is relatively straightforward. You can wipe it with a cloth moistened with water and a mild detergent, but you should avoid using a flammable cleaning agent such as ethanol on the outside of the unit.
  • The heating bath: This should also be cleaned with an appropriate solvent or water and a mild detergent. Note that some manufacturers advise not to use solvents on a bath, particularly those with Teflon coatings. Be sure that the bath is switched off before cleaning and that the evaporation flask, if still attached, is in the upper stop position.
  • Protective covers: These can be removed and cleaned, but note that they may scratch easily, so avoid using abrasive materials for cleaning. Covers made of protective glass may be sensitive to certain solvents, so it’s best to stick with water and a mild detergent.