Essential oils have become attractive candidates for use in the livestock industry, yet their mode of action over microbial populations of animals remains largely unknown. To gain further insight, this study investigated the bacterial population in segments of gastrointestinal tract and performance of pre-weaned dairy calves supplemented with a commercial Oregano extract containing essential oils. Ten Holstein calves weighing 37.1 kg ± 3.6 kg were fed 6 L/day of milk replacer, and had free access to water and calf starter ad libitum from the first day, and to hay ad libitum from the third week of the start of the study period. The calves were randomly assigned to two treatments: CON - without additive; and OR - 60 mg/kg body weight per day with oregano extract. Weaning occurred on the 53rd day of the experimental period and on the 54th day, all calves were euthanized, and their rumen, jejunum, cecum and colon contents were sampled to determinate bacterial population. The OR supplementation increased starter concentrate intake, but did not affect feed conversion, average daily gain (ADG), total VFA acetate, butyrate, and propionate ruminal concentrations, as well as C2 to C3 ratio. Apparent digestibility tended to increase in OR for DM, OM, NFCcp and CP. The alpha diversity analysis (Shannon index) indicated a higher diversity of rumen and jejunum bacterial population in OR calves. Oregano extract affected positively and negative the abundance of both positive and gram-negative bacteria in the gastrointestinal tract. Moreover, OR decreased potentially pathogenic genera such Streptococcus, Escherichia and Clostridium, albeit it also decreased the population of the potentially beneficial Bifidubacterium in the jejunum and cecum. Oregano extract supplemented to pre-weaned dairy calves modulates bacteria microbiota and may contribute to reduce pathogenic bacteria in the gastrointestinal tract.