A real-time annotation system and methodology for annotating measurement waveforms in a signal measurement system that includes a graphical user interface for displaying waveforms and measurement results on a signal measurement system display. Generally, he annotation system enables an operator to generate a graphical annotation label containing any desired data, and to graphically position the annotation label at any desired location on the measurement display, enabling the operator to positionally associate the graphical annotation label with a desired waveform or waveform feature displayed on the graphical user interface. The annotation system is constructed and arranged to enable an operator to graphically generate an annotation label containing operator-generated information and to graphically alter the position of the annotation label such that the annotation label is positionally associated with a desired feature of a waveform displayed on the graphical user interface. The annotation label may be implemented as dialog box, window or other display region in the graphical environment provided by the graphical user interface.