Background. In pigs, the ratio between lean mass and fat mass determines production efficiency and is strongly influenced by the number and size of cells in tissues. During growth, the increase in the number of cells results from the recruitment of different populations of multipotent adult stem cells residing in the tissues. We hypothesized that the impact of a hygiene challenge on the proportions of adult stem cells in adipose tissue and skeletal muscle may differ between pigs with different residual feed intake (RFI), a measure of feed efficiency. Methods. At the age of 11 weeks, Large White pigs from two lines divergently selected for low and high RFI were housed in two contrasting hygiene conditions (good vs poor). After six weeks of challenge, pigs were slaughtered (n = 5-9/group). Samples of subcutaneous adipose tissue and longissimus muscle were collected, and cells from the stromal vascular fraction (FSV), which includes adult stem cell populations, were isolated from each tissue. Adipose and muscle cell populations from the FSV were phenotyped by flow cytometry using antibodies that targeted different cell surface markers (CD45 to identify hematopoietic cells; CD34, CD38, CD56 and CD140a to identify mesenchymal stem cells (MSC) with adipogenic and/or myogenic potential). Results. Adipose tissue and muscle shared some common MSC populations although MSC diversity was higher in muscle than in adipose tissue. In muscle, the CD45- CD56+ CD34- CD140a+ and CD45- CD56+ CD34+ CD140a+ cell populations were abundant. Of these two cell populations, only the proportions of CD45- CD56+ CD34+ CD140a+ cells increased (P < 0.05) in pigs housed in poor hygiene compared with good hygiene conditions. For the CD45-CD56- CD34- cell population, present in low proportion, there was an interaction between hygiene condition and genetic line (P < 0.05) with a decrease in low RFI pigs housed in poor hygiene conditions. In adipose tissue, the two abundant MSC populations were CD45- CD56- CD34- and CD45- CD56+ CD34-. Moreover, the proportion of CD45- CD56- CD34- cells increased (P < 0.05) whereas the proportion of CD45- CD56+ CD34- tended to decrease (P < 0.1) in pigs housed in poor conditions. This study shows that the proportions of some MSC populations were affected by hygiene of housing conditions in a tissue-dependent manner in pigs of both RFI lines. Therefore, these cell populations could be targeted to modulate growth and body composition in growing animals.