The objective of this study was to determine the differences in bacterial diversities and compositions of rumen and feces between healthy cows and cows with indigestion, mastitis or laminitis. Forty-five lactating dairy cows including 10 healthy, 11 with indigestion, 13 with mastitis, and 11 with laminitis were enrolled. Bacterial communities were assessed using MiSeq Illumina sequencing of the 16S rRNA gene. One-way variance analysis and LSD multiple comparisons were used to compare microbial compositions and diversity indices between groups. A P < 0.05 was considered significant. Bacteroidetes and Firmicutes were the predominate phyla in both the rumen fluid and the feces. Indigestion reduced the diversity of fecal bacterial community, increased the diversity of ruminal bacterial community, and changed the relative abundance of Firmicutes in both the rumen and feces and that of Bacteroidetes in the feces. Although they did not influence the diversity, mastitis and laminitis altered the compositions of the ruminal and fecal bacterial community at different taxonomic level. At the phylum level, the relative abundance of Spirochaetes and Fibrobacteres in the rumen and Proteobacteria in the feces were increased (P < 0.05), and Firmicutes in the feces was reduced by the indigestion challenge; and the relative abundance of Bacteroidetes in the rumen was reduced and Firmicutes in the rumen was increased (P < 0.05) by the laminitis challenge. At the family level, the indigestion challenge increased the proportion of Porphyromonadaceae in rumen as well as Enterobacteriaceae and Bacillaceae in feces, and decreased the proportion of Lachnospiraceae in rumen (P < 0.05) as well as Clostridiaceae, Peptostreptococcaceae and Paenibacillaceae in feces (P < 0.05); the mastitis challenge increased the proportion of Porphyromonadaceae and others at lower percentages in rumen (P < 0.05), and increased the proportion of Bacillaceae in feces; the laminitis challenge increased the proportion of Prevotellaceae and reduced the proportion of Acidaminococcaceae in rumen (P < 0.05). Results from this study show that the fecal or rumen microbial compositions of dairy cows with indigestion, mastitis, and laminitis shifted compared with those in healthy cows.