Fragile X syndrome results from the lack of FMR1 expression. To understand how the lack of FMR1 function leads to the syndrome, we are studying the Drosophila FMR1 related protein (dFMR1). We performed affinity purification of dFMR1-associated complexes from cultured Drosophila S2 cells and found that dFMR1 associates with a key component of RNA interference, AGO2. Our finding suggests cross talk between the fragile X syndrome protein and RNA interference. In this chapter, we describe a tandem affinity purification method to isolate the protein components and small RNAs in the dFMR1-associated complexes.