Background <p>Large-scale deletions in mitochondrial DNA (mtDNA) have been associated with aging and degenerative diseases. It has been reported that increased oxidative stress in gingival tissue might cause damage to proteins, lipids and DNA and mtDNA deletion has been proposed as an early marker of oxidative DNA damage.</p> Methods <p>To investigate whether a common 5-kb deletion and other uncharacterized large-scale deletions within mitochondrial DNA (mtDNA) exist in molar–incisor periodontitis, we collected blood and gingival tissue genomic DNA samples from 20 patients with molar–incisor periodontitis (MIP, the same as the Aggressive Periodontitis, 1999 classification of periodontal diseases) and 20 age-matched healthy control subjects. We amplified the mtDNA deletions using nested and long-range polymerase chain reaction (PCR) with enhanced sensitivity assays. The levels of the common 5-kb deletion in total mtDNA were assessed by quantitative real-time PCR, and the deletions were identified by TA cloning and sequencing.</p> Results <p>We detected a novel 4,745-bp deletion (np8426–np13171), flanked by 18-bp imperfect repeats, in both blood and gingival tissue genomic DNA samples. The difference in the frequency of this deletion for the gingival tissue genomic DNA samples of the MIP group versus the control group was statistically significant (<i>P</i> = 0.008). The relative amount of the 4,745-bp deletion did not differ significantly between the two groups. The common 5-kb deletion also occurred in both groups at similar levels. 8-Hydroxydeoxyguanosine (8-OHdG) levels were higher in blood (<i>P</i> = 0.0009) and gingival tissue (<i>P</i> = 0.041) samples in the MIP group compared with the controls.</p> Conclusions <p>These observations suggest that the detection frequency of the novel 4,745-bp mtDNA deletion might be associated with molar–incisor periodontitis and a potential link with the high levels of 8-OHdG in the local pathological microenvironment of periodontal disease.</p>