A typical paradigm in the investigation of complex human disease is to assess the effects of cis-regulatory polymorphisms implicated in association studies on transcription in cellular expression systems. Evidence from in vitro transfection studies is often assumed to be sufficient evidence for the in vivo functional importance of a polymorphism in the context of human disease, even though many confounding effects (e.g. temporal regulation, tissue specificity, genetic background) are not considered. In this study, we evaluate this assumption directly by examining the translation of in vitro results on allele-specific expression to an in vivo system using four genes that have been well documented through reporter assays to have promoter polymorphisms affecting transcription level: monoamine oxidase A (MAOA), neuropeptide Y (NPY), endothelial nitric oxide synthase (NOS3), and prodynorphin (PDYN). In our study, MAOA was found to have large allelic imbalances, which indicates that there is in vivo variation in the expression of this gene. However, the imbalances observed were not correlated with genotype at the putatively functional polymorphism. PDYN, NOS3 and NPY did not have large allelic imbalances. Overall, there was no statistically significant effect of these polymorphisms on expression level as measured by imbalance ratios in any of these genes. These results suggest that the functional effects of a polymorphism on gene expression may be more complicated and context dependent than is often assumed and also imply that the use of cell-based expression studies to support the role of such polymorphisms in disease etiology should be treated with caution.