The present invention has its object to provide a control apparatus for an internal combustion engine including a variable valve operating mechanism which is capable of accurately and effectively identifying an abnormality-occurring cylinder during operation while preventing the deterioration of a catalyst. A fuel injection valve which is capable of injecting fuel for each cylinder is provided. Variable valve operating mechanisms which are capable of halting the operation of the intake and exhaust valves in the closed state for each cylinder are provided. An abnormality evaluation index value is acquired during the operation of the internal combustion engine and, based on the abnormality evaluation index value, an abnormality which has occurred in at least one cylinder in the internal combustion engine is detected. When the abnormality is detected, a cylinder halting to perform the halting of fuel supply and the halting of the valve operation in the closed state is executed with a first partial cylinder made up of at least two cylinders as the target. After the cylinder halting, with the cylinder to be halted being changed, a cylinder halting is executed with a second partial cylinder made up of at least one cylinder as the target. Based on the change in the abnormality evaluation index value associated with the changing of the cylinder to be halted, the abnormality-occurring cylinder is identified.