AbstractThis study aimed to examine the local embryo effect on the transcriptomic response of the epithelial cells of the oviduct in vivo. Fifteen heifers were synchronized and artificially inseminated to a standing heat. All heifers were slaughtered on Day 2.5 after oestrus. The oviducts from 13 animals were isolated, trimmed free of tissue and divided between ampulla/isthmus. The ipsilateral isthmus was divided into smaller sections (2 cm). Each section was sequentially flushed until the embryo was located (4/13) and then opened and scraped longitudinally to obtain the epithelial cells. Cells were snap‐frozen in LN2 for gene expression analysis. All recovered embryos were found at the beginning of the isthmus. The 2 cm sections selected for the transcriptomic analysis were as follows: embryo section (in which the embryo was found); proximal section (through which the embryo had passed); distal section (on the uterine side of the embryo); and contralateral section (section from the contralateral isthmus). The expression pattern of eight genes (STK32A, KERA, QRFPR, MCTP1, PRELP, VAT1L, SOCS3 and CCL20) differentially expressed between the isthmus of pregnant (multiple embryo model) and cyclic heifers were assessed by RT‐qPCR. One‐way ANOVA and t test was used for statistical analysis. Comparisons between ipsilateral and contralateral oviduct or along the ipsilateral oviduct resulted in no differences for all genes. Despite the failure to detect a site‐specific response of a single embryo on the abundance of distinct transcripts in the bovine oviduct in vivo on Day 2.5, the current methodology with proposed modifications would be useful for future studies to examine the local embryo effect.