Current diagnostics for community-acquired pneumonia (CAP) include testing for a wide range of pathogens, which is costly and not always informative. We compared clinical and laboratory parameters of patients with CAP caused by different groups of pathogens to evaluate the potential for targeted diagnostics and directed treatment. In a prospective study, conducted between April 2008 and April 2009, adult patients with CAP were tested for the presence of a broad range of possible respiratory pathogens using bacterial cultures, PCR, urinary antigen testing and serology. Of 408 patients with CAP, pathogens were detected in 263 patients (64.5%). Streptococcus pneumoniae and influenza A virus were the most frequently identified bacterial and viral pathogens, respectively. Age had a significant effect on the prediction of aetiology (P = 0.054), with an increase in the relative contribution of viruses with advancing age. Multivariate analyses further showed that the presence of cough increased the likelihood of detecting a viral pathogen [odds ratio (OR) 5.536, 95% confidence interval (CI) 2.130-14.390], the presence of immunodeficiency decreased the likelihood of detecting a bacterial pathogen (OR 0.595, 95 % CI 0.246-1.437) and an increase in pneumonia severity index score increased the likelihood of detecting a pathogen in general. Although several variables were independently associated with the detection of a pathogen group, substantial overlap meant there were no reliable clinical predictors to distinguish aetiologies. Therefore, testing for common respiratory pathogens is still necessary to optimize treatment.