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Virtual microscopy (VM) is a widely used teaching method in Medical Education in many developed countries. In Brazil, however, this is not the case for most medical schools, considering Brazilian social inequality and uneven access to technology. Recently, the Covid-19 pandemic has also challenged Universities to seek and make a transition toward more effective methods of full-time online education. Thus, the main goal of this work was to verify student's perception and academic performance, assessed upon VM implementation in a Brazilian Medical School. Ribeirao Preto Medical School students answered a 26-question survey with regards to optical microscopy (OM) and VM. Academic performance was compared between participants that were (year of 2019) or were not (year of 2015) exposed to VM. Taken the results together, subjective impressions such as handling, suitability, learning effectiveness, and pleasure using the tools, have shown a higher score for virtual microscopy (median = 29), when compared to optical microscopy (median = 24) with a P-value < 0.001 by Wilcoxon rank test, upon measurement using an ordinal scale. Regarding academic performance, no statistically significant differences were found between groups (P-value = 0.38, Cohen's d = 0.19). Therefore, VM proved to be adequate to the Brazilian medical education in light of Brazilian social contexts and Covid-19 pandemic.