Buttery spot has greatly affected coffee plants in field conditions. Its cause has been attributed to Colletotrichum gloeosporioides. However, its symptoms in leaves have not been reproduced. In this study we reported for the first time the presence of X. fastidiosa, causal agent of the coffee atrophy in petiole and hypocotyls from coffee plants with buttery spot through PCR and ultrastructural studies by scanning electron microscopy (SEM). In this study three trials were developed. In the first we collected leaves from plant with and without buttery spot symptoms in two places which were prepared for SEM. In the second petioles of 40 symptomatic and 40 asymptomatic leaves were collected in a coffee experimental field of Federal University of Lavras. Petiole from these leaves were cut and macerated for DNA extraction and analyzed by PCR. Four petioles of each sample (plants with and without symptoms) were prepared for SEM. In a third trial, seeds from plants with battery spot were sowed in foam trays with Plantimax (R) substrate. The trays stayed in a growth chamber and after 30,60 and 90 days of the germination hypocotyls were collected for preparation and observation in SEM. Initially a bacterium similar to X fastidiosa was found in vessels of symptomatic plants studied. Through the analysis by PCR we verified X. fastidiosa in 34% of plants with the disease symptoms and 9,3% in those without symptom of buttery spot. Petioles of positives Xylella plants by PCR presented obstruction of vessels of xylem by bacteria. Out of four PCR-negatives plants, one had petioles with vessels clogged by bacteria when analyzed by SEM. In analyzed hypocotyls with SEM were observed bacterial cells like X. fastidiosa in xylem vessels at 60 and 90 days. This is the first report of the colonization of X. fastidiosa in coffee plant petiole and hypocotyls of seeds of plants expressed buttery spot symptoms.