If your breast pump is like your lifeline you need to keep it clean too. An unclean breast pump could increase chances of contamination of breast milk and lead to a stomach infection or stomach flu. It could also lead to diarrhoea loose motions etc. So it is necessary to clean them once you are done with it. Here are few things that you need to follow: Make it a point to clean all the parts of the breast pump that come in contact with breast milk such as bottles valves and breast shields should be cleaned after each use.