The adjuvants (thimerosal, squaline, aluminum, etc.) and the sourcing of certain ingredients (animal DNA) used in vaccines have been my biggest concern as a parent. I also take any study with a grain of salt since funding plays a big role on the outcome/resulting data presented. A good resource for this reason is:http://www.corbettreport.com/episode-286-rockefeller-medicine/
Links to source materials are provided
I also came across a rather compelling logical argument from Jon Rappoport about vaccines: http://jonrappoport.wordpress.com/2013/02/05/dumbed-down-populations-accept-outrageous-vaccine-logic/