The present invention provides a method, apparatus, and computer instructions for organizing threads in an instant messaging session. Instant messages are received from a list of contacts. Each of these messages are stored in a set of folders, wherein each folders in the set of folders stores messages for a contact in the number of contacts. Each file is linked for access though a graphical user interface. Message threads are handled by displaying a primary dialog window, wherein the primary dialog window includes an ongoing conversation pane and an outgoing message pane. Responsive to a user input identifying a new thread, a secondary dialog window is displayed, wherein the secondary dialog window includes an ongoing conversation pane and an outgoing message pane. Responses to outgoing messages sent from the outgoing message pane are displayed in the primary dialog window in the ongoing conversation pane in the primary dialog window. Responses to outgoing messages sent from the outgoing message pane in the secondary dialog window are displayed in the ongoing conversation pane in the secondary dialog window, wherein the primary dialog window and the secondary dialog window.