I frequent a popular baby website on a daily basis and cloth diapers regularly come up. One of the questions I see asked on a regular basis is “how do I disinfect/sanitize my diapers?’. A lot of people think that human waste is full of diseases and that anything that touches is must be thoroughly disinfected in order to not spread disease. The truth is, unless your child is ill, simple washing with detergent after each use is plenty to remove the soiled matter and bacteria on the diapers.
This blog post explains clearly why disinfecting is not needed on a regular basis: http://www.ecobabysteps.com/2009/08/05/do-i-need-to-disinfect-my-cloth-diapers/
If you do find yourself with diapers that do need disinfecting due to illness or infection in the diaper area, there are lots of easy things you can do! For most bacteria, UV rays are enough to kill them, so sunning you diapers is an excellent idea and this has an added bonus of whitening those stains. If your problem is a little bit more complicated (yeast rash for example), refer to this awesome chart by CD manufacturer Thirsties: http://www.thirstiesbaby.com/blog/how-to-disinfect-your-diapering-products/