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Simple Summary: Selection for hyper-prolific sows has led to increased litter size, decreased birth weight, and increased within-litter variation. This is accompanied by impaired colostrum intake of piglets and poor performance. We aimed to investigate the total count of fecal lactobacilli and species diversity in growing pigs on two herds. Study pigs were categorized either small or large according to their birth weight. Sow colostrum quality and colostrum supply of piglets were determined. We hypothesized that the birth weight and growth performance of pigs are associated with fecal lactobacilli composition, which is influenced by colostrum. Small pigs had higher lactobacilli counts in both herds, but the difference was significant only for one herd (p = 0.01). Colostrum quality was numerically better in the herd that appeared also better managed in comparison to the other study herd. Colostrum intake tended to be significantly associated with the total lactobacilli count in the better-managed herd. In conclusion, herd-level factors clearly contribute to the microbiota of pigs, but birth weight also plays a potential role in the gastrointestinal tract lactobacilli dynamics. Our results revealed a potential long-term effect of colostrum, and therefore give a reason to investigate more thoroughly the associations between maternal immunity, pig microbiota, and performance. We studied the fecal lactobacilli count and species diversity of growing pigs along with immune parameters associated with intestinal lactobacilli. Thirty pigs categorized as small (S, n = 12) or large (L, n = 18) at birth were followed from birth to slaughter in two commercial herds, H1 and H2. Herds differed in terms of their general management. We determined sow colostrum quality, colostrum intake, piglet serum immunoglobulins, and pig growth. We took individual fecal samples from pigs in the weaning and finishing units. We studied lactobacilli count and identified their diversity with 16S PCR. Total lactobacilli count increased in H1 and decreased in H2 between samplings. Lactobacilli species diversity was higher in H1 in both fecal sampling points, whereas diversity decreased over time in both herds. We identified altogether seven lactobacilli species with a maximum of five (one to five) species in one herd. However, a relatively large proportion of lactobacilli remained unidentified with the used sequencing technique. Small pigs had higher lactobacilli counts in both herds but the difference was significant only in H2 (p = 0.01). Colostrum quality was numerically better in H1 than in H2, where colostrum intake tended to be associated with total lactobacilli count (p = 0.05). [ABSTRACT FROM AUTHOR]