While testing for uterine bacterial infection is usually performed prior to artificial insemination (AI), samples taken during or after embryo flushing are generally not assessed either in subfertile and old mares or in fertile mares, even though knowledge of the status of the uterine environment in which the embryo is to develop would help to predict the outcome of embryo transfer programmes. The presence of bacteria and inflammatory cells in the liquid retained in the filter after uterine flushing in donors was determined at the moment of embryo recovery. Primarily, a group of mares (n = 8) displaying evident clinical signs of endometritis was selected to evaluate the cytological and bacteriological findings in filters after uterine flushing and in uterine cotton swabs. Two uterine samples (for cytological and bacterial evaluation) were taken with cotton swabs and, subsequently, the uterus was flushed and the efflux was also subjected to bacteriological and cytological analysis. Later, a group of donors (n = 20) was also involved to evaluate the presence of bacteria and polymorphonuclear leukocytes (PMN). After embryo flushing and collection, the efflux retained in the filter was evaluated by cytology and bacteriology. A sterile cotton swab was then scrubbed on the filter mesh, and a bacterial culture was performed. The embryo recovery rate was 30% (n = 6); Escherichia coli was isolated in one efflux sample collected from embryo-productive flushings, while the other five samples were negative by culture. Bacterial growth (not considered as contamination) was observed in a total of three samples, although no inflammatory cells were detected. Bacteria were isolated in endometrial samples collected after embryo flushing in donor mares, although inflammatory cells were never present in the uterus of mares from which embryos were recovered. In the absence of clinical signs, cytological and/or bacteriological samplings are not very useful for estimating the success of embryo recovery in donor mares, but evaluation of the filter and efflux after uterine flushing in donors may provide valuable information regarding uterine status at embryo collection.