The inclusion of DNA polymorphism into paternity analysis represents a major advance since it allows one to achieve a high probability of exclusion. This is of particular importance in paternity cases in which the mother and the alleged father are close relatives. The purpose of this article is to demonstrate an approach to calculate the probability of exclusion and to compute the paternity index in case of father-daughter incest using data from multiallelic loci that can be obtained with a single locus probe. The global probability of exclusion achieved at a multiallelic locus, in cases of father-daughter incest, is lower than the one obtained when both parents are not relatives. The probability of exclusion of each mother-offspring pair is different from that obtained when the parents are not close relatives. Among mother-offspring pairs having the same genotype, the probability of exclusion is zero, and in such a condition, the locus is not informative. To obtain a high exclusion capability, it is necessary to analyze several independent loci in which both the mother and the child have different genotypes. Expressions to obtain the paternity index for all the possible combinations of mother-offspring-alleged father in cases of father-daughter incest are derived and discussed.