Genetic, biochemical and phenotypic diversity is a hallmark of OXPHOS deficiencies. Among the responses frequently reported for these deficiencies is differential expression of several genes involved in mitochondrial biogenesis. These responses are often associated with elevated oxygen radical production. The genetic diversity of tissue and cell lines used in these investigations, however, complicates the interpretation of observations. We investigated mtDNA copy number and selected transcriptional responses after inducing stable Rieske protein knockdown in 143B cells. Despite the significant loss of complex III activity, hydrogen peroxide levels remained comparable to controls. Furthermore, no significant change in mtDNA copy number was observed. Mitochondrial L-strand- and D-loop transcript levels remained unchanged, while the H-strand transcript for COXII was reduced. With the exception of mitochondrial single-stranded binding protein (mtSSB), which was reduced, no transcriptional changes of the mtDNA replication and transcription machinery were observed. Notably however, a selection of nuclear-encoded OXPHOS gene transcripts was generally reduced (statistically insignificant), except for NDUFS3 and COX4I1 transcripts, which were significantly reduced. From these results we conclude that the induction of a low superoxide producing complex III deficiency in 143B cells has an insignificant effect on mtDNA replication and function, but that expression of OXPHOS genes is generally down regulated. This may indicate a lowering of mitochondrial biogenesis and a shift towards anaerobic energy metabolism to improve cellular survival. ; http://dx.doi.org/10.1016/j.biochi.2011.01.004