We prospectively evaluated 639 sequential clinical isolates of alpha-hemolytic gram-positive cocci as possible Streptococcus pneumoniae. On the basis of results of tests for optochin susceptibility, tube bile solubility, and the quellung reaction, 74 strains (11.6%) were categorized as unequivocal pneumococci (optochin positive, tube bile solubility positive, quellung reaction positive). Among 450 optochin- and tube bile solubility-negative organisms, a subset of 56 strains was tested for quellung reaction (all negative); these isolates were categorized as unequivocal nonpneumococci. A final 115 organisms with an inconsistent or discordant combination of susceptibility to optochin, tube bile solubility, and quellung reaction were categorized as equivocal strains. With the unequivocal isolates, a commercial molecular probe for S pneumoniae (AccuProbe; Gen-Probe, San Diego, Calif) showed 100% sensitivity (74/74) and 100% specificity (56/56). Among the 115 equivocal strains, however, 33 (28.7%) reacted with the AccuProbe, whereas only 3 (2.6%) showed a capsule that reacted in the quellung test. A subset of the equivocal strains identified in this group of primarily respiratory isolates may have been S pneumoniae that only partially expressed their classic phenotype of optochin susceptibility and bile solubility and only rarely expressed capsular antigens. A practical, cost-sparing algorithm is proposed to facilitate the routine clinical identification of S pneumoniae.