To exert beneficial effects for the host, for example, improving the intestinal microflora, a probiotic must reach the intestine as a viable strain. These properties must be demonstrated by in vitro as well as in vivo methods. However, only a few well-designed human clinical studies have shown these properties. Lactobacillus johnsonii La1 has been shown to give many beneficial effects for the host, but it is unclear whether a viable strain of L. johnsonii La1 has the effect of improving host intestinal microflora. In the present study, a randomised double-blind placebo-controlled cross-over trial was conducted to elucidate the effect of L. johnsonii La1 on human intestinal microflora. Twenty-two young healthy Japanese women were randomly divided into two groups, and either received fermented milk with L. johnsonii La1 or a fermented milk without L. johnsonii La1 (placebo) daily for 21 d. Consumption of the fermented milk: (a) increased total Bifidobacterium and Lactobacillus, and decreased lecithinase-positive Clostridium in the faeces; (b) increased the faecal lactic acid concentrations; (c) decreased the faecal pH; (d) increased the defecation frequency. These changes were stronger than those observed with the placebo. L. johnsonii La1 was identified in all subjects only after the consumption of the fermented milk. These results suggest that L. johnsonii La1 can contribute to improve intestinal microflora with probiotic properties.