Recent reports have documented a decrease in anaerobic bacteremias and have questioned the need for routine anaerobic blood cultures. At the same time, we and others have noted an increase in fungal bloodstream infections. In this two-part study, we first compared recoveries of obligate anaerobic bacteria with those of fungi over a 13-year period and then examined the recoveries of all bacteria and fungi in aerobic and anaerobic blood culture bottles during a 12-month period. During the 13-year period, the number of patients with anaerobic bacteremia remained relatively constant (average, 39 patients per year), while the incidence of fungemia steadily increased, from 12 patients in 1978 to 117 patients in 1990. Of the 1,090 anaerobic isolates, 55.1 and 90.2% were recovered in aerobic and anaerobic bottles, respectively, compared with 98.6 and 37.0% of the 2,582 fungi. During the 12-month period of evaluation, 2,980 bacteria and fungi were recovered in cultures collected from 1,555 patients. Overall, 21.1% more organisms were recovered in aerobic bottles than in anaerobic bottles, including significantly more Staphylococcus species; gram-positive aerobic bacilli; Escherichia, Enterobacter, Pseudomonas, Xanthomonas, and Acinetobacter species; miscellaneous gram-negative bacilli; and yeasts. Only anaerobic gram-negative bacilli and non-spore-forming gram-positive bacilli were isolated more commonly in anaerobic bottles. These data support the concepts that bacteremia caused by obligate anaerobic bacteria is decreasing relative to sepsis caused by other bacteria and fungi and that the routine use of unvented anaerobic blood culture bottles reduces the recovery of common aerobic bloodstream pathogens.