An implantable device programmer includes a variety of features for allowing a clinician to perform an automated and customized follow-up examination of a patient having an implanted cardiac implantable device, the implantable device being of the type which captures and stores various types of diagnostic data for subsequent retrieval and evaluation. A custom protocol feature of the programmer allows the clinician pre-specify and then semi-automatically follow an ordered sequence of protocol steps, each protocol step involving the interrogation of the implantable device and the display by the programmer of associated implantable device data (such as a heart rate histogram, or the results of a ventricular capture test). When the clinician initiates a custom protocol, the programmer automatically retrieves all of the diagnostic data records of the protocol in the protocol order. This automatic retrieval is performed in the background, allowing the clinician to begin viewing the initial diagnostic data records of the protocol while the other items are being retrieved. Via a user interface of the programmer, the clinician can rapidly and efficiently sequence through the data display screens associated with the protocol, to thereby view the various diagnostic data records and/or perform the various diagnostic tests of the protocol.