A comma is always used to separate the day of the month from the year when the full date is written.
She was seen on January 12, 2010.
His last surgery was on June 15, 2009.
Do not use a comma when the month and year are written without a specific date.
She was seen in my office in January 2010.
His last surgery was in June 2009.
When the full date is dictated in mid-sentence, use a comma to separate the year from the rest of the sentence.
NOTE: This is consistent with the Chicago Manual of Style. The AMA Manual of Style doesn't contain sufficient information. The Gregg Reference Manual indicates that punctuation following the year is only used if the sentence structure otherwise requires it.
She was seen on January 12, 2010, in my office.
His last surgery was on June 15, 2009, a cholecystectomy.
Use a comma where a date and a number are adjacent to one another. The preference, however, is to recast the sentence and separate them for clarity.
In January of 2009, 500 cases of whooping cough were reported.
In January of 2009, there were 500 reported cases of whooping cough.