Microbial contamination of fuel has been the cause of several problems in transportation and storage of these products. Due to the lack of previous studies related to these problems in Costa Rica, bacterial quality was evaluated biannually in automotive fuels stored in the four oil distribution facilities of the Costa Rican Petroleum Refinery (RECOPE). In 12 oil storage tanks, for a total of 96 samples, mesophilic, heterotrophic aerobic/facultative counts (ASTM D6974-04) and identification of bacteria presented in regular gas, premium gas and diesel from the bottom and superior part of the tanks were done; in the samples containing an aqueous phase, sulfate reducing bacteria (SRB) were also quantified by the most probable number technique (MPN), according to the ASTM D4412-84 standard. The higher contamination was shown at the bottom of the tanks (populations up to 10(4) UFC/l), especially if there was accumulated water, in which case populations reached 10(8) UFC/l. The most contaminated fuel was diesel (counts up to 10(4) UFC/l), whereas the less contaminated was premium gas. The less contaminated fuels were from the facilities of La Garita and Barranca, whereas the most contaminated were from Ochomogo. Nevertheless, the quantified populations did not cause significant alteration in quality physicochemical parameters in the samples analyzed. A total of 149 bacterial strains were isolated, 136 (91.3%) Gram positive and 13 (8.7%) Gram negative. The most frequent genera were Staphylococcus (24.0%), Micrococcus (21.9%), Bacillus (18.8%) and Kocuria (11.5%) among Gram positive bacteria and Pseudomonas (7.3%) among Gram negative bacteria. The majority of these genera have been found as fuel contaminants or even as degraders of this kind of products; nevertheless, some species for which their appearance or growth in hydrocarbons have not been described were found with low frequencies. SRB were present in counts up to 10(5) MPN/l in 42.9% of water containing samples (including all from diesel tanks), indicating biocorrosion processes risk in fuel transport and storage systems. From the findings in this study it is recommended to give a frequent maintenance to fuel containers, based on continuous drainage and removal of accumulated water, antimicrobial agent addition and microbial quality monitoring in country’s fuels. Rev. Biol. Trop. 57 (3): 489-504. Epub 2009 September 30.<br>Se evaluó semestralmente durante dos años la calidad bacteriana de los combustibles almacenados en los cuatro planteles de la Refinadora Costarricense de Petróleo (Costa Rica). Para un total de 96 muestras se realizaron recuentos (norma ASTM D6974-04) e identificación de las bacterias presentes en gasolina regular, gasolina súper y diesel en los niveles superior e inferior de los tanques contenedores; en las muestras con fase acuosa se cuantificaron las bacterias reductoras de sulfato (SRB, norma ASTM D4412-84). La mayor contaminación se observó en el fondo de los tanques, sobretodo si se presentó una capa de agua almacenada. El diesel fue el combustible más contaminado, sin embargo, no se observó alteración importante en los parámetros fisicoquímicos de las muestras evaluadas. Se aislaron 149 cepas, 136 (91.3%) Gram positivas y 13 (8.7%) Gram negativas; los géneros más frecuentes fueron Staphylococcus (24.0%), Micrococcus (21.9%), Bacillus (18.8%), Kocuria (11.5%) y Pseudomonas (7.3%). Con bajas frecuencias se encontraron algunas especies para las que no se ha descrito su aparición o crecimiento en hidrocarburos. Las SRB se presentaron con recuentos de hasta 105 MPN/l en un 42.9% de las muestras con agua residual, principalmente en diesel, lo cual es indicativo de alerta por biocorrosión. A partir de los resultados se recomienda dar un mantenimiento frecuente a los contenedores, la adición de compuestos antimicrobianos y el monitoreo de la calidad microbiana de los combustibles del país