Two fundamental questions in stem cell research are what controls stem cell number in vivo and which signal pathways regulate self-renewal. Here we summarize our recent studies regarding the role of BMP signaling in regulation of stem cell behavior in both the hematopoietic and intestinal systems. These studies provide evidence to show that BMP signaling plays an important role in controlling stem cell number, at least in these two stem cell compartments. However, the BMP signal utilizes different mechanisms to fulfill this purpose: in the hematopoietic stem cell compartment it controls stem cell number through regulation of the niche size; in the intestinal stem cell compartment it directly controls self-renewal of stem cells through restriction of Wnt/beta-catenin activity. The Bmpr1a mutant mouse provided an elegant model which allowed us to identify the HSC niche, an enigma for more than 25 years. Our work provided more evidence to demonstrate the essential function of the niche in maintenance of stem cells and showed that multiple signals are required to maintain a balanced control of stem cell self-renewal.