Diarrhea is the most common affliction of young calves during the first weeks of life. Reasons for diarrhea are multifactorial, but we hypothesized that the composition of the microbiota inhabiting the gastrointestinal tract may act as a protective barrier or as a facilitator for colonization of the intestine by pathogenic bacteria or viruses. For a period of 2 mo, all healthy calves that entered a commercial contract heifer operation were enrolled in a sampling scheme consisting of collecting fecal samples from the rectum at arrival and at 30 d of life. Calves were checked daily by a veterinarian. After completing all samplings, calves were classified as HEALTHY if did not have diarrhea, or as DIA if they experienced at last one case of diarrhea. Calves from DIA and HEALTHY categories were randomly selected and their fecal samples processed to recover DNA. Then, the 16sRNA gene was sequenced (Illumina MiSeq 2X250) individually using barcoded primers. One animal from DIA and 3 from HEALTHY were excluded from sequencing due to poor DNA recovery. Thus, data presented herein correspond to 18 (7 HEALTHY and 11 DIA) Holstein female calves (44.2 ± 2.9 kg of initial BW). The Quantitative Insights Into Microbial Ecology software package was used to define operational taxonomic units (OTUs) and compare the community structures and taxonomical profiles of calves. The diversity within samples (α) and between groups (β) were estimated, and a discriminant analysis of OTUs at the genus level was performed between HEALTHY and DIA calves at arrival. First cases of diarrhea occurred at 19.3 ± 8.6 d of age. Alpha diversity increased with age (P < 0.05), but at arrival, calves in the HEALTHY category had greater (P < 0.05) α diversity than DIA calves at arrival. Based on the discriminant analysis, HEALTHY calves, in general, had greater abundance of Collinsella, Lactobacillus, Lachnospiraceae, Subdoligranulum, and Megasphaera, and lower abundance of Anaerostipes, Feacalibcaterium, and Ruminococcus than DIA calves. Management and nutritional practices that promote this microbiome pattern before 10 d of life may represent a potential alternative to minimize diarrhea.