Community-acquired pneumonia (CAP) accounts for more than two million deaths per year in children < 5 years of age. Recognition of pathogens is vital for guiding antibiotic treatment. In Gabon, no epidemiologic data on childhood CAP were available to help guide antibiotic therapy. We conducted a prospective, hospital-based, cross-sectional survey at the Albert Schweitzer Hospital, Lambarene, Gabon, to assess the importance of atypical organisms (Chlamydia pneumoniae, Mycoplasma pneumoniae, Bordetella pertussis, and Legionella pneumophila) and Streptococcus pneumoniae in the etiology of CAP in children by means of real-time polymerase chain reaction, cell culture, and serology. Collectively, atypical bacteria accounted for 11% of cases with a special emphasis on B. pertussis, accounting for 6% of cases. Clinical differentiation of atypical from typical pneumonia in children remains challenging. Molecular diagnostic methods offer fast and highly sensitive diagnostic tools and would be able to help guide antimicrobial therapy in rural areas where follow-up is difficult.