The objective of this prospective cohort study was to evaluate the effect of parity and uterine health status postpartum on the gene expression profile of the endometrium early post-partum. Twenty-four Holstein cows were randomly selected (16 multiparous (MP) and 8 primiparous (PP)) and endometrium biopsies were collected on days 1, 3, and 6 after calving and clinically monitored for metritis. Rectal temperature was measured twice and fever was defined as a temperature ≥39.5 °C. A case of metritis was diagnosed with the presence of red-brown watery, foul-smelling uterine discharge or a purulent discharge with more than 50% pus and fever between days 1 and 6 postpartum. Cows were then retrospectively selected (cows diagnosed with metritis were paired with healthy ones) to analyze the expression of 66 genes measured on the NanoString nCounter Analysis System. The genes selected were related with adhesion, immune system, steroid and prostaglandin biosynthesis regulation, insulin metabolism and transcription factors, and nutrient transporters. The results indicated a different pattern on genes related to immune function by parity. PTX3, involved in antigen presentation, was increased in healthy MP compared with healthy PP whereas inflammatory cytokine TNFα and complement-related protein SERPING1 was upregulated in MP compared with PP (P < 0.05). As expected, presence of a metritis condition affected the expression of genes related to immune function. There was an increased expression of the antiviral factor MX2 and MYH10 gene, which is involved in macrophages recruitment, in metritic compared with healthy cows (P < 0.05). Differences in uterine involution from cows diagnosed with metritis were reflected by the downregulation of IGF1 (P < 0.10), involved in endometrium remodeling, and a possible compensatory upregulation of its receptor IGFR1 (P < 0.05). A greater expression of prostaglandins and oxytocin receptors (PGR and OXTR), involved in the involution process, were observed in metritic PP compared with healthy PP (P < 0.05). Overall, it seems that metritis significantly modulate processes closely tied with the physical involution of the uterus early post-partum (IGF1, IGFR1, PGR, OXTR), whereas both metritis and multiparous cows tended to upregulate genes related to immune response (PTX3, TNFα, SERPING1, MX2, MYH10).