This paper deals with a mixed logit model for vaccination data. The effect of a newly developed vaccine for a certain chicken disease can be evaluated by a noninfection rate after injecting chicken with the disease vaccine. But there are a lot of factors that might affect the noninfecton rate. Some of these are fixed and others are random. Random factors are sometimes coming from the sampling scheme for choosing experimental units. This paper suggests a mixed model when some fixed factors need to have different experimental sizes by an experimental design and illustrates how to estimate parameters in a suggested model.