We investigated the nasopharyngeal carriage of Streptococcus pneumoniae and Staphylococcus aureus in 355 children hospitalized with severe pneumonia. Of the children, 239 (67.3%) were human immunodeficiency virus (HIV)-1 positive; 169 (47.6%) carried S. pneumoniae, 91 (25.6%) carried S. aureus, and 33 (9.3%) carried both. S. pneumoniae carriage was not related to HIV-1 status. The HIV-1-positive children had a significantly higher rate of S. aureus carriage than did the HIV-1-negative children (31.4% vs. 13.8%; P<.001). The rate of S. aureus carriage in the HIV-1-negative S. pneumoniae carriers was significantly lower than that in the noncarriers (5.5% vs. 21.3%; P=.013), but the rate of S. aureus carriage in the HIV-1-positive S. pneumoniae carriers was not significantly lower than that in the noncarriers (26.3% vs. 36.0%; P=.11). We did not find a negative association between S. pneumoniae and S. aureus carriage in HIV-1-positive hospitalized children with severe pneumonia.