Objective: To detect mRNA levels and expression of CD44, CD54, CD29 and E-cadherin (E-cad) and to discuss their relationship with formation and drug resistance of ovarian cancer SKOV3ip1 multicellular aggregates. Methods: Liquid overlay system was employed to obtain multicellular aggregates. mRNA levels and expression of CD44, CD54, CD29 and E-cad were investigated with RT-PCR and flow cytometry (FCM) respectively. Results: Compared with monolayer cells, RT-PCR results showed a decrease in CD44 mRNA level by 0.626-fold and a decrease in CD29 mRNA level by 0.792-fold in multicellular aggregates. However, an increase in CD54 mRNA level by 1.815-fold and an increase in E-cadherin mRNA level by 1.344-fold were found in multicellular aggregates. The results revealed the downregulation of CD44 and CD29 and the upregulation of CD54 and E-cad genes activity. CD44 expression in monolayer cells and multicellular aggregates were 75.995±3.046 and 50.700±9.351 (%) respectively and there was a significant decrease in multicellular aggregates (P=0.001). Compared with control cells, no expression of CD54 was detected in monolayer cells (P=0.563) but markedly elevated CD54 expression was detected in multicellular aggregates (15.780±2.217) (%) (P<0.01). High expression of CD29 was seen in monolayer cells and also in multicellular aggregates with positive rates of 96.290+1.201 (%) and 92.494±2.055 (%). However, the expression of CD29 in multicellular aggregates was significantly reduced (P=0.014). Also no expression of E-cadherin was found in monolayer cells compared with control cells (4.490±1.283) (%) (P=0.65) while significantly increased expression in aggregates cells (17.258± 5.572) (%) (P=0.003) was observed. Conclusion: Significant differences in mRNA levels and expression of CD44, CD54, CD29 and E-cadherin clearly exist between monolayer cells and multicellular aggregates, which may be associated with the formation of multicellular aggregates and its drug resistance.