ABSTRACT This study deals with the development of analytical methods for metabolic changes detection in short time terms upon stress conditions in fresh fruits such as fungal infection and mechanical impacts. Although modern post harvest techniques that are carried out nowadays and fungicides application in citric fruits in the manipulation lines, fungal infections occurrence are still very frequent in stored fruits through moulds spores germination in the citric fruits peel. This process is many times favoured by wounds and bruises produced in fruits due to mechanical impacts occurred during their manipulation. Such infections are detected traditionally by visual signs on citric fruits peel (“decay”) with consequent damage and complete decay of affected fruits; reduced price products and in many cases, no commercialization possibilities. Taking into account this situation, methods development that may collaborate in fungal infections prediction occurrence through metabolically changes detection prior to fungal infection evidence was considered of interest. And in this way be able to contribute for the development of optimization commercialization steps systems. Metabolic changes detection was oriented towards respiration rate analysis as well as the eventual occurrence of given off volatiles (acetaldehyde and ethanol). A head space gas chromatography analysing system was designed and implemented. For this purpose, a micro gas chromatograph (mCG) was connected to a hermetic respiration chamber containing the fruit to be analysed by automatic aspiration of gas samples in an almost continuous way at a prefixed time intervals and short time of analysis. The system was developed with fresh oranges var. Navelate. Afterwards, it was applied to oranges var. Navelate inoculated with spores from moulds that habitually cause the highest economically damage in citric fruits (Penicillium genus) stored at 21ºC and 75,5% RH or 85% RH and also in Granny Smith apples mechanically injured in controlled conditions, simulating possible mechanical impacts that fruits may receive in stores. Fungal inoculums came from cultures generated from pure lyophilised cultures obtained from the “Spanish Type Culture Collection”. A mathematical model that simulates the produced gas fluxes in the system is outlined in order to quantify the respiration rate and given off volatiles detected in each analysis. Results let correlate obtained respiration rates with fungal infection visual signs, being possible to detect increases in respiration rates prior visual infection signs detection in all analysed oranges, being more aggressive the P. digitatum treatment at 75,5% HR. In apples no respiration rates changes were detected which did not let correlacionate with other physicochemical changes in the fruits (colour parameters, texture and total soluble solids content). With these preliminary data, this methodology may constitute an interesting line to be continued to deep in about fungal infections predictions and mechanical impacts detections for the consequent shelf life fresh fruit optimization.