In a method for operating an internal combustion engine, the engine includes a plurality of cylinders each of which having at least one valve of a first type, an inlet valve, and at least one valve of a second type, an exhaust valve, arranged in an end part of the cylinder, each of the cylinders further having a piston movably arranged therein, the piston being adapted to reciprocate between a first end position and a second end position, wherein the first end position is located closer to the valves than the lower end position, the engine being adapted to allow deactivation of at least one cylinder by reducing its supply of fuel, the engine further being adapted to allow varying opening times of the inlet valves and/or the exhaust valves. The method includes extending the total opening time of at least one valve type of a deactivated cylinder compared to the opening time of the same valve type when the cylinder is active, the extension of the total opening time being performed such that at least one valve of the type is open at least partly both during a first engine stroke, wherein the piston moves in a direction towards its second end position, as well as during a second consecutive engine stroke, wherein the piston moves in a direction towards its first end position.