Acidity is an important environmental condition encountered by lactobacilli during food fermentation. In this report we show that triggering the stationary-phase acid tolerance response (ATR) in L. acidophilus CRL 639 depends on the final growth pH. In free-pH fermentation runs (final pH = 4.5), the cells were completely resistant to acid stress, whereas cells from cultures under controlled pH (pH = 6.0) were very sensitive. The relationship between the final pH and the development of cross-resistance to different kinds of environmental stress was also evaluated. The study of protein profiles showed the overexpression of 16 proteins from 6.5 to 70.9 kDa in stationary phase cells. Seven of these proteins (26.3, 41.4, 48.7, 49.3, 54.5, 56.1, and 70.9 kDa) were expressed as result of the stationary phase itself, while nine proteins (14.1, 18.6, 21.5, 26.9, 29.3, 41.9, 42.6, 49.6, and 56.2 kDa) were exclusively induced as a result of the drop in culture pH during free fermentation runs. These results strongly suggest the involvement of these proteins in cell adaptation to environmental changes.