A driveshaft misalignment measurement system for a drivetrain of an aircraft includes a driveshaft having a first end forming a driveshaft spline and a drivetrain subsystem including a spline adapted to connect to the driveshaft spline to form a splined connection. Rotational energy is transferred between the drivetrain subsystem and the driveshaft via the splined connection. The driveshaft misalignment measurement system also includes accelerometers coupled to the drivetrain configured to detect acceleration data and a flight control computer configured to measure misalignment at the splined connection using the acceleration data.