The regulation of alternative transcripts of the NDUFS4 gene of complex I of the respiratory chain has been studied in human cell lines. One of the alternative transcripts (SV1) is subjected to the NMD degradation pathway which involves the hUPF1 and hUPF2 factors. Another transcript (SV3) appears to be controlled in the nuclear fraction and to be enhanced when hUPF1 is depleted, but unaffected by translation inhibitors or when hUPF2 expression is down-regulated. A pathological homozygous nonsense mutation in exon 1, found in a patient affected by mitochondrial disorder, inactivated in the patient's fibroblasts NMD degradation of SV1 and enhanced the nuclear production of SV3. In another patient with a homozygous splice acceptor site mutation in intron 1, SV3, which was the only transcript of NDUFS4 gene to be produced, accumulated in fibroblasts.