Assays of micronucleus are extensively used in genotoxicity testing and in monitoring of human exposure to genotoxic materials. As nuclear buds could be a new source of micronuclei formed in interphase, the assay of contents of nuclear bud in normal and comparison group is needed. In this paper, we proposed a new automatic nuclear buds detection algorithm based on ellipse fitting. Experimental results show that our algorithm is effective and efficient. We believe that this is the first report on automated nuclear bud detection for DNA damage scoring.