Objectives: To compare groups of etiologic agents for neonatal fungemia based on previously published case reports with regard to case outcomes. Methods: Secondary analysis of data from case reports published in scientific literature indexed in Medline, Scopus and LILACS databases, and starting from the year, full texts were registered until the year 2010. Results: Thirty-four species of fungi were isolated in 252 cases reported over a 40-year period. The distribution of fungal groups according to the development level of a case’s region of origin was very uneven (p < 0.001), with a predominance of C. albicans and other fungi (Aspergillus sp.) in more developed countries. However, 73% of the chi-squared distribution corresponded to differences observed in the frequency of Candida sp. and non-albicans Candida. While the frequency of candidemia by C. albicans was progressively declining in the period from 1966 to 2010, reports of non-albicans candidemia and other non-Candida fungi became significantly (p < 0.00001) more frequent over the course of the period studied. As for the outcome of death, it was statistically more frequent (p < 0.02) in cases where non-albicans Candida or non-Candida fungi were isolated. Conclusion: fungi of the genera Candida and Aspergillus were the etiologic agents most frequently identified in published cases of neonatal fungemia; the outcome of death was more often related to cases where non-albicans Candida or non-Candida fungi were isolated.