An increasingly popular and promising way for??complex disease diagnosis is to employ artificial neural networks(ANN). Single Nucleotide Polymorphisms (SNP) data from individuals is used as the inputs of ANN to find out specific SNP patterns related to certain disease. Due to the large number of SNPs, it is crucial to select optimal SNP subset and their combinations so that the inputs of ANN can be reduced. With this observation in mind, a hybrid approach –a combination of genetic algorithms (GA) and ANN (called GANN) is used to automatically determine optimal SNP set and optimize the structure of ANN. The proposed GANN algorithmis evaluated by using both a synthetic dataset and a real SNP dataset of a complex disease.