In another question, I asked about pasteurization of raw milk at home. I got some interesting comments (of course, I further searched on the internet) that some people prefer not to pasteurize raw milk to keep its original flavor and nutrition properties. Pasteurization (whether industrial or at home) at 63 - 72 C will cause a significant loss of vitamins, useful ingredients and generally nutrition values of milk.  Not only for the sake of pasteurization, but also we boil milk for preparing hot drinks. Of course, the boiling point is not necessary, and we let it to cool down a little bit.  Is it really bad to let milk boil? Does it significantly reduce the nutrition values? 
So long as we are discussing this topic.  The Center for Disease Control has a specific answer for your question and their answer is NO.  However, According to this paper from the National Center for Biotechnology Information pasteurization causes a breakdown in milk-caesin protein which after uptake through Peyer's patch can promote allergic sensitivity.  There are other controversial claims that the higher temperatures required for milk pasteurization and boiling breaks down some of the ingredients with negative effects.  There is a rebuttal to the FDA note from realmilk.com that counters the FDA facts with other scientific papers.  However, it's been noted that their paper may not be heavily grounded in rigorous scientific data.  There is a more idepth look in this presentation to British Columbia Centre for Disease Control seems to cover the spectrum of myths based on scientific evidence and critiques.  Some of the points discussed are:   Raw Milk is not a high-risk food (in today's age). Raw Milk does have protective properties to allergies and Asthma. also noted in this NCBI paper The notion of "the loss of nutrients due to pasteurization is insignificant" is based on an antiquated nutritional paradigm. Pasteurization and temperature does reorganize some of the milk proteins, but the effects of that is unknown.   You may wish to watch the presentation, the gist of the discussion start at about 8 minutes in.  In the end, if you believe pasteurization has negative nutritional effects, then boiling raw milk will, too (minus the safety of pasteurized milk).   