Excluding these charges, the firm would have made a fourth quarter profit of $3.78bn.
Sales from the division which includes Vista, launched in January, rose 14% to $38.1bn in the past three months.
Total sales rose 13% to $13.3bn over the same period.
Microsoft said it had had an extremely strong year.
"Surpassing $50bn in annual sales is a testament to the innovation and value that our product groups delivered into the marketplace," said chief operating officer Kevin Turner.
In the upcoming year, Microsoft said it expected sales to rise to between $56bn and $57bn.
Microsoft shares rose nearly 2% before it announced its results but fell in after-hours trading amid concerns it had only met market expectations not exceeded them.
