The purpose of the study is to compare the mRNA expression of pro-apoptotic and anti-apoptotic genes by using the GeneSystem 320 (Capital Genomix Inc., Gaithersburg, MD) to examine the differential expression in Ewing sarcoma and neuroblastoma cell lines. This is an alternate method for which internal controls have been built into the system for comparing mRNA. The tumor cell lines were chosen based on their previously characterized Fas-resistance or Fas-sensitive properties in order to determine the differences in their response to apoptotic signals. Two representative pro-apoptotic genes (BAD and SMAC) and one anti-apoptotic gene (BAR) were chosen for the study. The results of mRNA expression were correlated with protein expression by Western analysis. BAD was highly expressed in the Fas-sensitive cell lines while SMAC was equally expressed in both Fas-sensitive and Fas-resistant cell lines. On the other hand, BAR was highly expressed in Fas-resistant cell lines and minimally expressed in the Fas-sensitive cell lines. Our data suggests that levels of BAD and BAR mRNA expression predict sensitivity to apoptosis.