Alternative oxidase holds an enigmatic role in cellular metabolism. The effect of auxin-induced parthenocarpy of tomato fruits on the transcript accumulation of three genes, belonging to two-gene families, and on the immunolocalization of the protein of alternative oxidase were studied. The genes of the alternative oxidase 1 family were transcribed more abundantly in seeded fruits than in parthenocarpic ones during the climacteric fruit period. Moreover, there was a clearly distinctive pattern of transcript accumulation between genes of alternative oxidase 1 and alternative oxidase 2 families. Maximum accumulation of alternative oxidase gene transcripts coincided with the climacteric rise of respiration in mature green and breaker stages, whereas alternative oxidase 2-gene transcript accumulation was highest in immature green fruits. After postharvest storage of fruits close to plantation for 120 h and at 5°C, the relative transcript accumulation of all studied genes significantly increased in both fruit types; the effect, however, on seeded and on parthenocarpic fruits was not of the same level. The immunolocalization of alternative oxidase protein revealed a strong presence of alternative oxidase in the developing seeds. In conclusion, considerable differences were found in the regulation of alternative oxidase between seeded and parthenocarpic fruits during their development and postharvest storage.