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The aim of this work was to achieve a better understanding of the bacterial pathogens associated with stillbirths that would serve to inform clinical interventions directed at reducing this adverse pregnancy outcome. A prospective observational study was conducted with the participation of 22 women from northern Peru, of whom 11 experienced fetal death in utero and 11 delivered preterm births. Swabs were taken from the vagina, placenta, amniotic fluid and axilla of the infant at birth by Caesarean section. The bacterial populations in the vagina and the amniotic space of each participant were determined by employing the amplicon sequencing of the V4 region of the <i>16S rRNA</i> genes. The sequence data were analysed using bioinformatics tools. The work showed differences in the composition of the genital microbiomes of women who experienced preterm birth or fetal death in utero. There were no differences in the alpha diversity between the genital microbiotas of both groups of women, but there were more different taxa in the vagina and amniotic space of the preterm participants. <i>Lactobacillus</i> spp. was less abundant in the stillbirth cases. <i>E</i>. <i>coli</i>/<i>Shigella</i>, <i>Staphylococcus</i>, <i>Gardnerella</i>, <i>Listeria</i> and <i>Bacteroides</i> taxa were associated with the stillbirths. In each woman, there was a minimal concordance between the bacterial populations in the vagina and amniotic space.