This research aimed to determine the probability vector of Hardy‘s matrix for the homozygous (AA , aa ) and heterozygous (Aa), the proportions of individuals whose has those genotypes with their probabilities and the Hardy‘s matrix represented. Then the genotype frequencies of individual, whose affected by the diseases (eye, respiratory and skin) which are took place, as a result from the chemical attack are determined.Also in order to find the effect of genotypes on the diseases a particular transition probability matrix of hidden Markov Chain is prepared, and the transition probabilities for successive generations with the genotype frequencies of the individuals performed.The sample size of (500) have chosen by stratify random sampling from a list of (929) patients which are recorded by ministry of Martyr and Anfal.The steady stead of Hardy‘s matrix obtained after initial generation of diseases, also the transition probabilitymatrix of hidden Markov chain stabilized from generation (11) and the genotype vector took steady stead for diseases. Finally the Bayes‘ theorem applied to define the effects genotypes on (eye, respiratory, and skin) diseases