This study investigated the effects of a single amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses until the age of nine weeks. We also studied whether the treatment was associated with growth and mortality, the need for treatment of other diseases, the proportions of ampicillin resistant coliforms and antimicrobial resistance patterns of intestinal Escherichia coli (E. coli). A total of 7156 piglets, from approximately 480 litters, were divided into two treatment groups: ANT (N = 3661) and CON (N = 3495), where piglets were treated with or without a single intramuscular injection of 75 mg amoxicillin one day after birth, respectively. The umbilical and inguinal areas of weaned pigs were palpated at four and nine weeks of age. At the same time, altogether 124 pigs with hernias or abscesses and 820 non-defective pigs from three pens per batch were weighed individually. Mortality and the need to treat piglets for other diseases were recorded. Piglet faecal samples were collected from three areas of the floors of each pen at four weeks of age. The prevalence of umbilical hernias or abscesses did not differ between the groups at four weeks of age, but it was higher in the CON group than in the ANT group at nine weeks of age (2.3% vs. 0.7%, P < 0.05). Numbers of inguinal hernias and abscesses did not differ between the groups at four or nine weeks of age. The ANT group, when it compared with the CON group, increased the weight gain between four and nine weeks of age (LS means ± SE; 497.5 g/d ± 5.0 vs. 475.3 g/d ± 4.9, P < 0.01), and decreased piglet mortality (19.5% ± 1.0 vs. 6.9% ± 1.0, P < 0.05) and the need to treat the piglets for leg problems (3.4% ± 0.3 vs. 1.9% ± 0.3%, P < 0.01) but not for other diseases by the age of four weeks. The proportion of ampicillin resistant intestinal coliform bacteria and the resistance patterns of the E. coli isolates were not different between the ANT and CON groups. In conclusion, our results showed that the amoxicillin treatment of new-born piglets produced statistically significant effect in some of the parameters studied. However, as these effects were only minor, we did not find grounds to recommend preventive antibiotic treatment. Further, continuous antimicrobial treatment of newborn piglets could negatively influence the development of the normal microbiota of the piglet and promote selection of antimicrobial resistance genes in herds. Therefore we suggest rejection of the use of routine administration of antimicrobial agents at birth.