Another good piece of advice is to specify your lots when selling partial positions, and keep track of them.  I have my trading program set on a "last in first out" default so any stocks that I maintain for a while I can get the long term gains even if I am trading around a core. If your accountant has the records he/she can maximize your tax benefits.  This also helps with wash sales.  The key defense against the IRS in trading gains/losses is accurate record keeping.