Abstract: Flux balance analysis and phenotypic data were used to provide clues to the relationships between the activities of gene products and the phenotypes resulting from the deletion of genes involved in respiratory function in S. cerevisiae. The effect of partial or complete respiratory deficiency on ethanol production and growth characteristics of hap4*/hap4*, mig1*/mig1*, qdr3*/qdr3*, pdr3*/pdr3*, qcr7*/qcr7*, cyt1*/cyt1* and rip1*/rip1* mutants, grown in micro-aerated chemostats, was investigated. The study provided additional evidence for the importance of the selection of a physiologically relevant objective function, and it may improve quantitative predictions of exchange fluxes as well as qualitative estimations of changes in intracellular fluxes. Ethanol production was successfully predicted by FBA in the case of qdr3*/qdr3* with maximization of ethanol production as the objective function, suggesting an additional role for Qdr3p in respiration. The absence of similar changes in estimated intracellular fluxes in qcr7*/qcr7* when compared to rip1*/rip1* and cyt1*/cyt1* indicated that the effect of the deletion of this subunit of the complex III was somehow compensated. Analysis of predicted flux distributions indicated self-organization of intracellular fluxes to avoid NAD(+)/NADH imbalance in rip1*/rip1* and cyt1*/cyt1* but not qcr7*/qcr7*. The flux through the glycerol efflux channel, Fps1p, was estimated to be zero in all strains under the investigated conditions. This indicates that previous strategies for improving ethanol production, such as the overexpression of the glutamate synthase GLT1 in GDH1 deletion background, or deletion of glycerol efflux channel FPS1 and over-expression of GLT1 are unnecessary in a respiratory deficient background.