Objective To examine the difference of mRNA expression in S180 cell strain and its different cloned cells.Methods The probes labeled by biotin were used in situ hybridization to detect the expression of 6 kinds of mRNA that were p16, c fos, c jun, c myc, p21 and p53.Results P16,c fos, c jun and c myc mRNAs were found in Cancer Institute S180 cells, c fos and c jun mRNAs in S1B11 cloned cells, c fos, c myc and c jun mRNAs in S2D9 cloned cells. Conclusion The expression of mRNAs was different in Cancer Institute S180 and 2 different cloned cell strains and c myc probe could distinguish S1B11 from S2D9 cloned cells; expression of mRNAs was associated with carcinogenesis.