will the short sale negatively effect my credit score?

In almost all cases, yes. How much can vary greatly depending on many factors. Your credit report will show the mortgage paid off, but settled for less than full amount (short sale). Other factors include if there were late payments before the short-sale, Your credit score before the even, number of other good or bad tradelines, and more. Short-sale generally hurts less than a foreclosure, but in the end, you caused a lender to suffer a loss. When getting a new loan, there will be a mandatory automatically denied period generally at least two-years, and up to four years before you can qualify for any new traditional mortgage loans, although you might be able to get a new sub-prime higher interest rate loan with a big down payment right away.