More than 98% of the pregnancies in South American camelids is carried out in the left uterine horn (LUH). Hence, embryos originated from right-ovary ovulations have to migrate to the contralateral or left uterine horn (LUH) to implant and survive. A reason for this unique pattern of embryo implantation has not been elucidated yet. In general, embryo implantation involves an extensive extracellular matrix (ECM) remodeling within the endometrium, in which collagen and matrix metalloproteinases (MMPs) play an essential role. Deregulation of collagen and MMPs has been related to embryo implantation failure, miscarriage, and infertility. Therefore, we hypothesized that ECM components in camelids could be involved in differential embryo implantation and consequently the high incidence of left horn gestations. The aim of this study was to describe and compare changes in ECM components in the left and right uterine horn of non-pregnant and 15 days pregnant alpacas. To test this hypothesis, the collagen content was evaluated by specific staining with Picrosirius Red and using ImageJ 1.42q software. Subsequently, gene expression of the following components of the MMP pathway was determined: MMP-2, -3, -7, -9, and -14, MMP substrates (COL1A2 and COL3A1), MMP inhibitors (TIMP1 and TIMP2), LGMN, an MMP activator, and EMMPRIN, an extracellular matrix metalloproteinase inducer. Uterine horns of pregnant alpacas exhibited a marked decrease in collagen content. In contrast, transcript expression of COL1A2 and COL3A1 was higher in the LUH of pregnant alpacas. Gene expression of MMP-3, -7, -9, -14, LGMN, and EMMPRIN were also higher in the LUH of pregnant animals, whereas MMP-2 gene expression was higher in the LUH of both pregnant and non-pregnant alpacas. Expression of TIMP1 and TIMP2 increased during pregnancy, with higher values in the LUH. In conclusion, expression of ECM components displayed a specific pattern depending on the uterine side and the physiological status (pregnant vs non-pregnant) of the animal. The increased expression of ECM transcripts in the left uterine horn during early pregnancy in alpacas suggests the involvement of these molecules in a highly regulated process leading to the implantation process.