Aim To assess whether there was a difference in the frequency of symptoms and signs among children with community‐acquired pneumonia (CAP) with viral or bacterial infection. Methods A prospective cross‐sectional study was conducted in Salvador, Brazil. Children less than 5‐years‐old hospitalized with CAP were recruited. Viral or only bacterial infection was diagnosed by an investigation of 11 viruses and 8 bacteria. Bacterial infection was diagnosed by blood culture, detection of pneumococcal DNA in acute buffy coat, and serological tests. Viral infection was diagnosed by detection of respiratory virus in nasopharyngeal aspirate and serological tests. Viral infection comprised only viral or mixed viral‐bacterial infection subgroups. Results One hundred and eighty‐eight patients had a probable etiology established as only viral (51.6%), mixed viral‐bacterial (30.9%), and only bacterial infection (17.5%). Asthma was registered for 21.4%. Report of wheezing (47.4% vs 21.2%; P = 0.006), rhonchi (38.0% vs 15.2%; P = 0.01), and wheezing detected on physical examination (51.0% vs 9.1%; P < 0.001) were the differences found. Among children with asthma, detected wheezing was the only different finding when children with viral infection were compared with those with only bacterial infection (75.0% vs 0%; P = 0.008). By multivariable analysis, viral infection (AdjOR 95% CI: 9.6; 95%CI: 2.7‐34.0), asthma (AdjOR 95% CI: 4.6; 95%CI: 1.9‐11.0), and age (AdjOR 95% CI: 0.95; 95%CI: 0.92‐0.97) were independently associated with wheezing on physical examination. The positive predictive value of detected wheezing for viral infection was 96.3% (95% CI: 90.4‐99.1%). Conclusion Wheezing detected on physical examination is an independent predictor of viral infection.