Pulmonary function is a crucial factor associated with longevity. Mitochondrial DNA 5178 cytosine/adenine (Mt5178 C/A) polymorphism is reported to be associated with longevity in the Japanese population. We have previously reported that Mt5178 C/A polymorphism is widely associated with physiological and biochemical status. The objective of this study was to investigate whether Mt5178 C/A polymorphism is associated with pulmonary function. The subjects were 463 Japanese men (mean age ± SD 54.0 ± 7.6 years). Genotyping of Mt5178 C/A was performed by polymerase chain reaction-restriction fragment length polymorphism. A cross-sectional study of the relationship between genotype and spirometric data, namely forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV₁), was conducted. Among younger subjects (age <55 years), FVC and FEV₁ were significantly higher for men with Mt5178A than for those with Mt5178C. Interaction between Mt5178 C/A polymorphism and smoking habits in FEV₁/FVC ratio was observed. Cigarette consumption (pack-years of smoking) was significantly and negatively associated with FEV₁/FVC ratio for men with Mt5178C. Among older subjects (age ≥55 years), FEV₁/FVC ratio was significantly lower for current smokers with Mt5178C than for never smokers with Mt5178C or for never smokers with Mt5178A. Mt5178 C/A polymorphism and its interaction with cigarette consumption may be associated with pulmonary function in Japanese men.