Objective: Knowledge of the microbial composition of deciduous endodontic infections is limited. This study aimed to evaluate the presence of the 10 oral bacterial species in samples from primary tooth root canals by using microarray technology and to determine the association of these organisms with clinical conditions. Study Design: The samples were collected from 30 root canals of primary teeth with primer infection. The bacterial composition of the samples was semi-quantitatively defined using a microarray system (Parocheck (R)). Results: All the tested species were detected in the samples. Fusobacterium nucleatum was the most frequently isolated bacterium (96.7%), followed by Prevotella intermedia (86.7%), Parvimonas micra (83.3%), Treponema denticola (76.7%) and Tannerella forsythia (66.7%). These bacteria were also present in high levels. All pairs of bacterial species were positively associated (RR>1), except P.intermedia and P.micra. On average, five species (range:3-8) were detected per amplified sample. Root canals of teeth with >5 different species were statistically associated with periapical radiolucency (P=0.049). Conclusions: Primary teeth with endodontic infections show a highly diverse variety of bacteria, in which the most prevalent specie are present in high proportions. The well-directed use of the improved microarray technology will provide additional valuable information for causative factors associated with endodontic diseases, helping to develop more successful antibacterial or anti-inflammatory treatment strategies.