Background: We investigated the utilization of cell free microbial DNA (cfDNA) at a Children's Hospital. Materials and Methods: cfDNA results were assessed regarding the contribution to therapeutic decisions. Results: Of 80 tests on 59 children, 1 test was unevaluable. At least one agent was identified in 45/79 (57%) tests from 34/59 (58.2%) children, 34/79 (43.0%) were negative in 31/59(52.5%) children. Of 45 positive results, 24/79 (30%) were contributory, 15/79 (19%) were diagnostic, 6/79 (7.6%) were diagnostic but diagnosis could have been made with other testing modalities, and 3/79 (3.8%) were diagnostic with minimal previous workup. 21/79 (26.6%) positives were noncontributory. Of 35 negative results, 9/79 (11.4%) were contributory, 26/79 (33.0%) were noncontributory. Efficiency was 30.4-41.8%. cfDNA detected agents not detected by conventional techniques in 22/79 (27.8%), detected different agents in 9/79 (11.4%), and failed to detect agents identified by conventional techniques in 4 (5%). Conclusions: Efficiency of cfDNA was 30.4-41.8.