Objective: To determine whether the duration of bacteremia among patients in the NICU, as well as risk of thrombocytopenia, differed between those with a central line associated bloodstream infection (CLABSI) due to a hetero-resistant vancomycin-intermediate Staphylococcus epidermidis (hVISE) and those whose CLABSI was due to vancomycin-susceptible S. epidermidis (VSSE). Methods: This retrospective cohort study covering the period from November 2009 through April 2014 examined records for 114 patients with coagulase-negative staphylococci (CoNS) CLABSI from two tertiary-care NICUs in Québec. Results: Of 111 patients included in the final analysis, 98 had an hVISE infection. The median duration of bacteremia was 4 days (range 0–33 days) for patients with hVISE and 4 days (range 2–8 days) for patients without hVISE. The duration of bacteremia was not significantly different between those with and without hVISE infection (B=−0.56, 95% CI −2.76 to 1.65). Further, the risk of thrombocytopenia for patients with and without hVISE was not significantly different (OR 0.42, 95% CI 0.076 to 2.72). Conclusions: hVISE was not shown to be associated with a longer duration of bacteremia or a greater risk of thrombocytopenia. This suggests that hVISE may not have a greater clinical impact than VSSE in infants with CLABSI. However, due to the small number of patients with VSSE in our cohort, firm conclusions cannot be drawn. Larger, multi-centre studies are needed to assess the true clinical relevance of vancomycin-intermediate hetero-resistant coagulase-negative staphylococci (hVICoNS) and before concluding on the need for hV identification in a clinical laboratory.