A method and a test instrument are provided for measuring program clock reference (PCR) jitter in a data stream, such as an MPEG-2 transport stream. The test instrument includes a line interface circuit for receiving the data stream, a digital computer for processing the data stream, a local clock for generating timestamps and a display unit. The digital computer extracts from the data stream a PCR sample which represents a count of a system time clock used to generate the data stream. The timestamp is obtained from the local clock and is associated with the PCR sample value. The digital computer determines a line of best fit to a set of values including the PCR sample value and the timestamp, and previously received PCR sample values and associated timestamps. The line of best fit represents a reconstructed system time clock. The digital computer determines a PCR jitter value for the PCR sample value by determining a distance between the line of best fit and the PCR sample value. The PCR jitter value may be displayed on the display unit, preferably in a histogram.