The influence of a non-circular cross section of a preform on the measurement of the refractive index was investigated. The deviation of the refractive index value from the value for a circular cross section can be both positive and negative depending on the rotational orientation of the preform. Therefore, the measurement is done at many rotational angles and the refractive index is calculated by averaging over the angles. The best solution was to define a number of layers and calculate the thickness and index for each layer in the preform. This was done for each angle and then the average of all index values for all angles was calculated. With this approach, the obtained refractive index is almost independent of the ovality for a variation of the diameter of ±10%.