Inference of biological networks from high-throughput data is a central problem in bioinformatics. Particularly powerful for network reconstruction is data collected by recent studies that contain both genetic variation information and gene expression profiles from genetically distinct strains of an organism. Various statistical approaches have been applied to these data to tease out the underlying biological networks that govern how individual genetic variation mediates gene expression and how genes regulate and interact with each other. Extracting meaningful causal relationships from these networks remains a challenging but important problem. In this paper we use causal inference techniques to infer the presence or absence of causal relationships between yeast gene expressions in the framework of graphical causal models. We evaluate our method using a well studied dataset consisting of both genetic variation information and gene expressions collected over yeast strains. Our predictions of causal regulators are consistent with previously known experimental evidence. In addition, our method can distinguish between direct and indirect effects of variation on a gene expression level.