The rapid evolution of techniques for measuring gene expression makes available substantial data which require careful analysis. In particular, relative quantification based on microfluidic cards allows performing of rapid large scale analyses. In the present study, we employed ovarian carcinoma cell lines resistant to cisplatin (IGROV-1/Pt1) or to a camptothecin (IGROV-1CPT/L), both characterized by a complex pattern of resistance to multiple agents, to examine the expression of genes of the superfamily of ATP binding-cassette (ABC) transporters by TaqMan microfluidic cards with the aim of developing an analytical tool to process data in this particular framework. The transcript quantification was based on the comparative threshold cycle method, which compares the expression of a target gene normalized to the expression of one or more reference genes (relative quantification). To process expression of ABC transporters, we applied a statistical procedure based on multivariate approaches and re-sampling techniques. The transporters that were significantly modulated included members of the ABCA, ABCB, ABCC and ABCG subgroups. A consistent up-regulation of ABCC2 as compared with the parental IGROV-1 cell line was observed in the IGROV-1/Pt1 cells, whereas down-regulation of ABCC6 and ABCG1 was found in IGROV-1/CPT-L cells. The use of rigorous analytic tools for gene expression data in preclinical models may lead to the identification of signatures to test in ovarian carcinoma clinical samples. Moreover, the developed procedure may be useful in the analysis of relative quantification data obtained with microfluidic cards in different experimental settings.