Partial volume (PV) is the effect of having a mixture of tissues present within a voxel. This effect occurs in tissue borders and affects small structures such as small multiple sclerosis (MS) lesions. Ignoring PV effects in volumetry may lead to significant estimation errors. Here, we propose a novel automated MS lesion segmentation technique that takes PV effects into account. The proposed method shows higher accuracy in terms of lesion volume estimation compared to a manually segmented ground truth as well as significant improvement in detection of small lesions, also in comparison to two software packages for MS lesion segmentation.