In paternity test using the DNA evidence, the analysis of the deficient case that the DNA profiles of mother or alleged father are not available is different from that of the trio case analyzed routinely. However, the motherless case that the genotypes of mother is not available has been requested and analyzed like the trio case. In this paper, we compared the motherless case and the trio case through the mean exclusion chance describing the probability of exclusion for a genetic marker system and the distribution of the probability of paternity calculated using the three current methods. We have also shown a case which can be falsely discriminated if it were requested in the analysis of the motherless case, and conclude that the analysis of the motherless case should be carefully conducted and the level for the discrimination should be different from that of the trio case.