An apparatus for diagnosing and controlling an ignition system of an internal combustion engine includes an ignition coil controllable by an ignition control circuit, a spark voltage sensor electrically connected to the high tension side of the ignition coil secondary and an ion voltage sensor electrically connected to the low tension side of the ignition coil secondary. A computer processes the spark voltage signal by comparing the signal to a number of predefined spark voltage waveforms in memory. If the spark voltage signal matches any of the spark voltage waveforms in memory that correspond to a predefined ignition system failure mode, a corresponding error code is stored in memory. The computer is further operable to process a voltage peak of the spark voltage, wherein the voltage peak corresponds to the breakdown voltage in the spark gap of a spark plug connected to the secondary coil. If the voltage peak exceeds a peak threshold, or if a slope of the spark voltage waveform about the voltage peak is less than a slope threshold, the computer is operable to store a corresponding error code in memory. The computer is also operable to process the ion voltage signal to determine a combustion quality value and a roughness value therefrom. If the combustion quality factor is outside a predefined range or if the roughness value exceeds a roughness threshold, the computer is operable to adjust engine fueling, spark timing and/or spark energy.